Screening methods for colon cancer depend on detecting either precancerous changes such as certain kinds of polyps or on finding early and thus more treatable cancer. The extent to which screening procedures reduce the incidence of gastrointestinal cancer or mortality depends on the rate of precancerous and cancerous disease in that population. gFOBT (guaiac fecal occult blood test) and flexible sigmoidoscopy screening have each shown benefit in randomized clinical trials. Evidence for other colon cancer screening tools such as iFOBT (immunochemical fecal occult blood test) or colonoscopy is substantial and guidelines have been issued by several advisory groups but does not include randomized studies.

In 2009 the American College of Gastroenterology (ACG) suggest that colon cancer screening modalities that are also directly preventive by removing precursor lesions should be given precedence, and prefer a colonoscopy every 10 years in average-risk individuals, beginning at age 50. The ACG suggests that cancer detection tests such as any type of FOB are an alternative that is less preferred, and if a colonoscopy is declined, the FIT (fecal immunochemical test, or iFOBT) should be offered instead. Two other recent guidelines, from the US Multisociety Task Force (MSTF) and the US Preventive Services Task Force (USPSTF), while permitting immediate colonoscopy as an option, did not categorize it as preferred. The ACG and MSTF also included CT colonography every five years, and fecal DNA testing as considerations. All three recommendation panels recommended replacing any older low-sensitivity, guaiac-based fecal occult blood testing (gFOBT) with either newer high-sensitivity guaiac-based fecal occult blood testing (hs gFOBT) or fecal immunochemical testing (FIT). MSTF looked at six studies that compared high sensitivity gFOBT (Hemoccult SENSA) to FIT, and concluded that there was no clear difference in overall performance between these methods.

The American College of Gastroenterology has recommended the abandoning of gFOBT testing as a colorectal cancer screening tool, in favor of the fecal immunochemical test. Though the FIT test is preferred, even the guaiac FOB testing of average risk populations may have been sufficient to reduce the mortality associated with colon cancer by about 25%. With this lower efficacy, it was not always cost effective to screen a large population with gFOBT.

If colon cancer is suspected in an individual (such as in someone with an unexplained anemia) fecal occult blood tests may not be clinically helpful. If a doctor suspects colon cancer, more rigorous investigation is necessary, whether or not the test is positive.

In 2006, the Australian Government introduced the National Bowel Cancer Program which has been updated several times since; targeted screening will be done of all Australians aged over 50 to 74 by 2017–2018. Cancer Council Australia recommended that FOBT should be done every two years. Gradually government fund disbursement meant that some people are not yet eligible for the national program and should pay for a FOBT by themselves.

The Canadian Cancer Society recommends that men and women age 50 and over have a FOBT at least every 2 years.

In colon cancer screening, using only one sample of feces collected by a doctor performing a digital rectal examination is discouraged.

The use of the M2-PK Test is encouraged over gFOBT for routine screening as it may pick up tumors that are both bleeding and non bleeding. It is able to pick up 80 percent of colorectal cancer and 44 percent for adenoma > 1 centimeter, while gFOBT picks up 13 to 50 percent of colorectal cancers.

An extensive literature has examined the clinical value of FOBT in iron deficiency anemia.

The tests that are considered to evaluate of the passage of blood in the stool are based on the characteristics of bleeding (color, quantity) and whether or not the person passing blood has a low blood pressure with elevated heart rate, as opposed to normal vital signs. The following tests are combined to determine the causes of the source of bleeding.

- Digital rectal exam (DRE) and fecal occult blood test (FOBT)

- Colonoscopy

- Anoscopy

- Esophagogastroduodenoscopy (EGD)

- Capsule endoscopy

- CT Scan

Melena is defined as dark, tarry stools, often black in color due to partial digestion of the RBCs.

Hematochezia is defined as bright red blood seen in the toilet either inside of, or surrounding the stool.

Hematochezia is typically presumed to come from the lower portion of the GI tract, and the initial steps of diagnosis include a DRE with FOBT, which if positive, will lead to a colonoscopy. If the person has a large amount of blood in their stool, an EGD test may be necessary. If no source of active bleeding is found on these examinations, a capsule endoscopy may be performed, in order to more closely examine the small bowel, which cannot be seen with the other types of studies. With melena, a DRE with FOBT is often also performed, however the suspicion for a source from the upper GI tract is higher, leading first to the use of EGD with the other tests being required if no source is identified. The anoscopy is another type of examination, which can be used along with a colonoscopy, which exams the rectum and distal portion of the descending colon.

Anemia is a common complication of blood in the stool, especially when there is a large amount of blood or bleeding occurs over a long period of time. Anemia is also commonly associated with an iron deficiency, due to the importance of iron in the formation of red blood cells (RBCs). When anemia is diagnosed as a result of blood in the stool, vitamins that are important for RBC formation (folate, vitamin B12, and vitamin C) are frequently prescribed in order to ensure that all the materials are available for those cells that are made.

An intussusception is often suspected based on history and physical exam, including observation of Dance's sign. A digital rectal examination is particularly helpful in children, as part of the intussusceptum may be felt by the finger. A definite diagnosis often requires confirmation by diagnostic imaging modalities. Ultrasound is the imaging modality of choice for diagnosis and exclusion of intussusception, due to its high accuracy and lack of radiation. The appearance of target sign (also called "doughnut sign" on a sonograph, usually around 3 cm in diameter, confirms the diagnosis. The image seen on transverse sonography or computed tomography is that of a doughnut shape, created by the hyperechoic central core of bowel and mesentery surrounded by the hypoechoic outer edematous bowel. In longitudinal imaging, intussusception resembles a sandwich.

An x-ray of the abdomen may be indicated to check for intestinal obstruction or free intraperitoneal gas. The latter finding implies that bowel perforation has already occurred. Some institutions use air enema for diagnosis, as the same procedure can be used for treatment.

An intussusception has two main differential diagnoses: acute gastroenteritis and rectal prolapse. Abdominal pain, vomiting, and stool with mucus and blood are present in acute gastroenteritis, but diarrhea is the leading symptom. Rectal prolapse can be differentiated by projecting mucosa that can be felt in continuity with the perianal skin, whereas in intussusception the finger may pass indefinitely into the depth of the sulcus.

Reducing opiate-based medication (when possible, tolerable, and safe; prescription medication changes should be done under the supervision of a physician), and adequate intake of liquids (water) and dietary fiber and daily exercise.

In a cecal volvulus, the cecum may be returned to a normal position and sutured in place, a procedure known as cecopexy. If identified early, before presumed intestinal wall ischemia has resulted in tissue breakdown and necrosis, the cecal volvulus can be detorsed laparoscopically.

There is no cure for short bowel syndrome except transplant. In newborn infants, the 4-year survival rate on parenteral nutrition is approximately 70%. In newborn infants with less than 10% of expected intestinal length, 5 year survival is approximately 20%. Some studies suggest that much of the mortality is due to a complication of the total parenteral nutrition (TPN), especially chronic liver disease. Much hope is vested in Omegaven, a type of lipid TPN feed, in which recent case reports suggest the risk of liver disease is much lower.

Although promising, small intestine transplant has a mixed success rate, with postoperative mortality rate of up to 30%. One-year and 4-year survival rate are 90% and 60%, respectively.

It is important to note that both barium enema and colonoscopy are contraindicated during acute episodes of diverticulitis, as the barium may leak out into the abdominal cavity, and colonoscopy can cause perforations of the bowel wall.

Treatment for sigmoid volvulus may include sigmoidoscopy. If the mucosa of the sigmoid looks normal and pink, place a rectal tube for decompression, correct any fluid, electrolyte, cardiac, renal or pulmonary abnormalities and then take the person to the operating room for repair. If surgery is not performed, there is a high rate of recurrence.

For people with signs of sepsis or an abdominal catastrophe, immediate surgery and resection is advised.

The treatment of fecal impaction requires both the remedy of the impaction and treatment to prevent future recurrences. Decreased motility of the colon results in dry, hard stools that in the case of fecal impaction become compacted into a large, hard mass of stool that cannot be expelled from the rectum.

Various methods of treatment attempt to remove the impaction by softening the stool, lubricating the stool, or breaking it into pieces small enough for removal. Enemas and osmotic laxatives can be used to soften the stool by increasing the water content until it is soft enough to be expelled. Osmotic laxatives such as magnesium citrate work within minutes - 8 hours for onset of action, and even then they may not be sufficient to expel the stool.

Osmotic laxatives can cause cramping and even severe pain as the patient's attempts to evacuate the contents of the rectum are blocked by the fecal mass. Polyethylene glycol (PEG 3500) may be used to increase the water content of the stool without cramping; however, since it may take 24 to 48 hours for it to take effect, it is not well suited to cases where the impaction needs to be removed immediately due to risk of complications or severe pain. Enemas (such as hyperosmotic saline) and suppositories (such as glycerine suppositories) work by increasing water content and stimulating peristalsis to aid in expulsion, and both work much more quickly than oral laxatives.

Because enemas work in 2–15 minutes, they do not allow sufficient time for a large fecal mass to soften. Even if the enema is successful at dislodging the impacted stool, the impacted stool may remain too large to be expelled through the anal canal. Mineral oil enemas can assist by lubricating the stool for easier passage. In cases where enemas fail to remove the impaction, polyethylene glycol can be used to attempt to soften the mass over 24–48 hours, or if immediate removal of the mass is needed, manual disimpaction may be used. Manual disimpaction may be performed by lubricating the anus and using one gloved finger with a scoop-like motion to break up the fecal mass. Most often manual disimpaction is performed without general anaesthesia, although sedation may be used. In more involved procedures, general anaesthesia may be used, although the use of general anaesthesia increases the risk of damage to the anal sphincter. If all other treatments fail, surgery may be necessary.

Individuals who have had one fecal impaction are at high risk of future impactions. Therefore, preventative treatment should be instituted in patients following the removal of the mass. Increasing dietary fiber, increasing fluid intake, exercising daily, and attempting regularly to defecate every morning after eating should be promoted in all patients.

Often underlying medical conditions cause fecal impactions; these conditions should be treated to reduce the risk of future impactions. Many types of medications (most notably opioid pain medications, such as codeine) reduce motility of the colon, increasing the likelihood of fecal impactions. If possible, alternate medications should be prescribed that avoid the side effect of constipation.

Given that all opioids can cause constipation, it is recommended that any patient placed on opioid pain medications should be given medications to prevent constipation before it occurs. Daily medications can also be used to promote normal motility of the colon and soften stools. Daily use of laxatives or enemas should be avoided by most individuals as it can cause the loss of normal colon motility. However, for patients with chronic complications, daily medication under the direction of a physician may be needed.

Polyethylene glycol 3350 can be taken daily to soften the stools without the significant risk of adverse effects that are common with other laxatives. In particular, stimulant laxatives should not be used frequently because they can cause dependence in which an individual loses normal colon function and is unable to defecate without taking a laxative. Frequent use of osmotic laxatives should be avoided as well as they can cause electrolyte imbalances.

Hematochezia is the passage of fresh blood through the anus, usually in or with stools (contrast with melena). Hematochezia is commonly associated with lower gastrointestinal bleeding, but may also occur from a brisk upper gastrointestinal bleed. The difference between hematochezia and rectorrhagia is that, in the latter, rectal bleeding is not associated with defecation; instead, it is associated with expulsion of fresh bright red blood without stools. The phrase bright red blood per rectum (BRBPR) is associated with hematochezia and rectorrhagia. It is also important to differentiate from hematopapyrus - blood on the toilet paper noticed when wiping. The term is from Greek αἷμα ("blood") and χέζειν ("to defaecate").

In adults, most common causes are hemorrhoids and diverticulosis, both of which are relatively benign; however, it can also be caused by colorectal cancer, which is potentially fatal. In a newborn infant, haematochezia may be the result of swallowed maternal blood at the time of delivery, but can also be an initial symptom of necrotizing enterocolitis, a serious condition affecting premature infants. In babies, haematochezia in conjunction with abdominal pain is associated with intussusception. In adolescents and young adults, inflammatory bowel disease, particularly ulcerative colitis, is a serious cause of haematochezia that must be considered and excluded.

Hematochezia can be due to upper gastrointestinal bleeding. However, as the blood from such a bleed is usually chemically modified by action of acid and enzymes, it presents more commonly as black "tarry" feces known as melena. Haematochezia from an upper gastrointestinal source is an ominous sign, as it suggests a very significant bleed which is more likely to be life-threatening.

Beeturia can cause red colored feces after eating beets because of insufficient metabolism of a red pigment, and is a differential sign that may be mistaken as hematochezia.

Consumption of dragon fruit or pitaya may also cause red discoloration of the stool and sometimes the urine (pseudohematuria). This too, is a differential sign that is sometimes mistaken for hematochezia.

In infants, the Apt test can be used to distinguish fetal hemoglobin from maternal blood.

Other common causes of blood in the stool include:

- Colorectal cancer

- Crohns disease

- Ulcerative colitis

- Other types of inflammatory bowel disease, inflammatory bowel syndrome, or ulceration

- Rectal or anal hemorrhoids or anal fissures, particularly if they rupture or are otherwise irritated

- "Shigella" or shiga toxin producing "E. coli" food poisoning

- Necrotizing enterocolitis

- Diverticulosis

- Salmonellosis

- Upper gastrointestinal bleeding

- Peptic ulcer disease

- Esophageal varices

- Gastric cancer

- Intense exercise, especially a high-impact activity like running in hot weather.

Doctors can diagnose proctitis by looking inside the rectum with a proctoscope or a sigmoidoscope. A biopsy is taken, in which the doctor scrapes a tiny piece of tissue from the rectum, and this tissue is then examined by microscopy. The physician may also take a stool sample to test for infections or bacteria. If the physician suspects that the patient suffers from Crohn's disease or ulcerative colitis, colonoscopy or barium enema X-rays are used to examine areas of the intestine.

There is no single, specific test for malabsorption. As for most medical conditions, investigation is guided by symptoms and signs. A range of different conditions can produce malabsorption and it is necessary to look for each of these specifically. Many tests have been advocated, and some, such as tests for pancreatic function are complex, vary between centers and have not been widely adopted. However, better tests have become available with greater ease of use, better sensitivity and specificity for the causative conditions. Tests are also needed to detect the systemic effects of deficiency of the malabsorbed nutrients (such as anaemia with vitamin B12 malabsorption).

A physical examination should involve at least an abdominal exam and rectal exam. Abdominal exam may reveal an abdominal mass if there is significant stool burden and may reveal abdominal discomfort. Rectal examination gives an impression of the anal sphincter tone and whether the lower rectum contains any feces or not. Rectal examination also gives information on the consistency of the stool, the presence of hemorrhoids, blood and whether any perineal irregularities are present including skin tags, fissures, anal warts. Physical examination is done manually by a physician and is used to guide which diagnostic tests to order.

The Rome III Criteria for functional constipation must include two or more of the following and present for the past three months, with symptoms starting for at least 6 months prior to diagnosis.

- Straining during defecation for at least 25% of bowel movements

- Lumpy or hard stools in at least 25% of defecations

- Sensation of incomplete evacuation for at least 25% of defecations

- Sensation of anorectal obstruction/blockage for at least 25% of defecations

- Manual maneuvers to facilitate at least 25% of defecations

- Fewer than 3 defecations per week

- Loose stools are rarely present without the use of laxatives

- There are insufficient criteria for irritable bowel syndrome

Diagnosis of angiodysplasia is often accomplished with endoscopy, either colonoscopy or esophagogastroduodenoscopy (EGD). Although the lesions can be notoriously hard to find, the patient usually is diagnosed by endoscopy. A new technique, pill enteroscopy, has been a major advance in diagnosis, especially in the small bowel which is difficult to reach with traditional endoscopy. With this technique a pill that contains a video camera and radio transmitter is swallowed, and pictures of the small intestine are sent to a receiver worn by the patient. Recently, multiphase CT angiography (without positive oral contrast) has been shown to play a promising role in the diagnoses of small and large bowel angiodysplasia, especially when associated with active hemorrhage

Angiodysplasiae in the small bowel can also be diagnosed and treated with double-balloon enteroscopy, a technique involving a long endoscopic camera and overtube, both fitted with balloons, that allow the bowel to be accordioned over the camera.

In cases with negative endoscopic findings and high clinical suspicion, selective angiography of the mesenteric arteries is sometimes necessary, but this allows for interventions at time of the procedure. An alternative is scintigraphy with red blood cells labeled with a radioactive marker; this shows the site of the bleeding on a gamma camera but tends to be unhelpful unless the bleeding is continuous and significant.

A high-fiber diet and fiber supplements are advisable to prevent constipation. The American Dietetic Association recommends 20–35 grams each day. Wheat bran has been shown to reduce intra colonic pressure.

The US National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) says foods such as nuts, popcorn hulls, sunflower seeds, pumpkin seeds, caraway seeds, and sesame seeds have traditionally been labeled as problem foods for people with this condition; however, no scientific data exists to prove this hypothesis. The seeds in tomatoes, zucchini, cucumbers, strawberries, raspberries, and poppy seeds, are not considered harmful by the NIDDK.

One study found that nuts and popcorn do not contribute positively or negatively to patients with diverticulosis or diverticular complications.

Often, a diagnosis can be made based on the patient's description of their symptoms, but other methods which may be used to verify gastritis include:

- Blood tests:

- Blood cell count

- Presence of "H. pylori"

- Liver, kidney, gallbladder, or pancreas functions

- Urinalysis

- Stool sample, to look for blood in the stool

- X-rays

- ECGs

- Endoscopy, to check for stomach lining inflammation and mucous erosion

- Stomach biopsy, to test for gastritis and other conditions

Symptoms of short bowel syndrome are usually addressed with medication. These include:

- Anti-diarrheal medicine (e.g. loperamide, codeine)

- Vitamin, mineral supplements and L-glutamine powder mixed with water

- H2 blocker and proton pump inhibitors to reduce stomach acid

- Lactase supplement (to improve the bloating and diarrhoea associated with lactose intolerance)

In 2004, the USFDA approved a therapy that reduces the frequency and volume of total parenteral nutrition (TPN), comprising: NutreStore (oral solution of glutamine) and Zorbtive (growth hormone, of recombinant DNA origin, for injection) together with a specialized oral diet. In 2012, an advisory panel to the USFDA voted unanimously to approve for treatment of SBS the agent teduglutide, a glucagon-like peptide-2 analog developed by NPS Pharmaceuticals, who intend to market the agent in the United States under the brandname Gattex. Teduglutide had been previously approved for use in Europe and is marketed under the brand Revestive by Nycomed.

Surgical procedures to lengthen dilated bowel include the Bianchi procedure, where the bowel is cut in half and one end is sewn to the other, and a newer procedure called serial transverse enteroplasty (STEP), where the bowel is cut and stapled in a zigzag pattern. Heung Bae Kim, MD, and Tom Jaksic, MD, both of Children's Hospital Boston, devised the STEP procedure in the early 2000s. The procedure lengthens the bowel of children with SBS and may allow children to avoid the need for intestinal transplantation. As of June 2009, Kim and Jaksic have performed 18 STEP procedures. The Bianchi and STEP procedures are usually performed by pediatric surgeons at quaternary hospitals who specialize in small bowel surgery.

Diagnosis is usually performed by submitting multiple stool samples for examination by a parasitologist in a procedure known as an ova and parasite examination. About 30% of children with "D. fragilis" infection exhibit peripheral blood eosinophilia.

A minimum of three stool specimens having been immediately fixed in polyvinyl alcohol fixative, sodium acetate-acetic acid-formalin fixative, or Schaudinn's fixative should be submitted, as the protozoan does not remain morphologically identifiable for long. All specimens, regardless of consistency, are permanently stained prior to microscopic examination with an oil immersion lens. The disease may remain cryptic due to the lack of a cyst stage if these recommendations are not followed.

The trophozoite forms have been recovered from formed stool, thus the need to perform the ova and parasite examination on specimens other than liquid or soft stools. DNA fragment analysis provides excellent sensitivity and specificity when compared to microscopy for the detection of "D. fragilis" and both methods should be employed in laboratories with PCR capability. The most sensitive detection method is parasite culture, and the culture medium requires the addition of rice starch.

An indirect fluorescent antibody (IFA) for fixed stool specimens has been developed.

1. One researcher investigated the phenomenon of symptomatic relapse following treatment of infection with "D. fragilis" in association with its apparent disappearance from stool samples. The organism could still be detected in patients through colonoscopy or by examining stool samples taken in conjunction with a saline laxative.

2. A study found that trichrome staining, a traditional method for identification, had a sensitivity of 36% (9/25) when compared to stool culture.

3. An additional study found that the sensitivity of staining was 50% (2/4), and that the organism could be successfully cultured in stool specimens up to 12-hours old that were kept at room temperature.

The following diagnostic methods are not routinely available to patients. Researchers have reported that they are more reliable at detecting infection, and in some cases can provide the physician with information to help determine whether "Blastocystis" infection is the cause of the patient's symptoms:

Serum antibody testing: A 1993 research study performed by the NIH with United States patients suggested that it was possible to distinguish symptomatic and asymptomatic infection with "Blastocystis" using serum antibody testing. The study used blood samples to measure the patient's immune reaction to chemicals present on the surface of the "Blastocystis" cell. It found that patients diagnosed with symptomatic "Blastocystis" infection exhibited a much higher immune response than controls who had "Blastocystis" infection but no symptoms. The study was repeated in 2003 at Ain Shams University in Egypt with Egyptian patients with equivalent results.

Fecal antibody testing: A 2003 study at Ain Shams University in Egypt indicated that patients symptomatically infected could be distinguished with a fecal antibody test. The study compared patients diagnosed with symptomatic "Blastocystis" infection to controls who had "Blastocystis" infection but no symptoms. In the group with symptoms, IgA antibodies to "Blastocystis" were detected in fecal specimens that were not present in the healthy control group.

Stool culture: Culturing has been shown to be a more reliable method of identifying infection. In 2006, researchers reported the ability to distinguish between disease causing and non-disease causing isolates of "Blastocystis" using stool culture. "Blastocystis" cultured from patients who were sick and diagnosed with "Blastocystis" infection produced large, highly adhesive amoeboid forms in culture. These cells were absent in "Blastocystis" cultures from healthy controls. Subsequent genetic analysis showed the "Blastocystis" from healthy controls was genetically distinct from that found in patients with symptoms. Protozoal culture is unavailable in most countries due to the cost and lack of trained staff able to perform protozoal culture.

Genetic analysis of isolates: Researchers have used techniques which allow the DNA of "Blastocystis" to be isolated from fecal specimens. This method has been reported to be more reliable at detecting "Blastocystis" in symptomatic patients than stool culture. This method also allows the species group of "Blastocystis" to be identified. Research is continuing into which species groups are associated with symptomatic (see Genetics and Symptoms) blastocystosis.

Immuno-fluorescence (IFA) stain: An IFA stain causes "Blastocystis" cells to glow when viewed under a microscope, making the diagnostic method more reliable. IFA stains are in use for Giardia and Cryptosporidium for both diagnostic purposes and water quality testing. A 1991 paper from the NIH described the laboratory development of one such stain. However, no company currently offers this stain commercially.

Symptoms of pouchitis include Increased stool frequency, urgency, incontinence, nocturnal seepage, abdominal cramping, pelvic discomfort, and arthralgia.

Symptom severity does not always correlate with severity of endoscopically- or histologically-evaluated pouch inflammation. Additionally, these symptoms are not necessarily specific for pouchitis, asthey may arise from other inflammatory or functional pouch disorders such as Crohn's disease of the pouch, cuffitis, pouch sinus, or irritable pouch syndrome. The most reliable tool for diagnosis is endoscopy combined with histologic features (derived from tissue biopsies obtained during endoscopy).