Investigations are performed to exclude other conditions:

- Stool microscopy and culture (to exclude infectious conditions)

- Blood tests: Full blood examination, liver function tests, erythrocyte sedimentation rate, and serological testing for coeliac disease

- Abdominal ultrasound (to exclude gallstones and other biliary tract diseases)

- Endoscopy and biopsies (to exclude peptic ulcer disease, coeliac disease, inflammatory bowel disease, and malignancies)

- Hydrogen breath testing (to exclude fructose and lactose malabsorption)

The differential diagnosis includes colon cancer, inflammatory bowel disease, ischemic colitis, and irritable bowel syndrome, as well as a number of urological and gynecological processes.

For diagnosis, measures of liver biochemistry and pancreatic enzymes are performed. Along with ruling out structural abnormalities, normally by performing an abdominal ultrasound and endoscopic retrograde cholangiopancreatography (ERCP). Measurements of bile transit when performing ERCP are taken to help evaluate different treatment options.

Sphincter of Oddi dysfunction is best diagnosed using manometry-an internal test done to measure the pressures within surrounding ducts to determine whether or not the muscle is functioning normally.

Studies have shown that up to 70% of IBS patients benefited from eating a low FODMAP diet. Symptoms most likely to improve from such a diet include urgency, flatulence, bloating, abdominal pain, and altered stool output. One national guideline advises a low FODMAP diet for managing IBS when other dietary and lifestyle measures have been unsuccessful. This diet restricts various carbohydrates which are poorly absorbed in the small intestine, as well as fructose and lactose, which are similarly poorly absorbed in those with intolerances to them. Reduction of fructose and fructan has been shown to reduce IBS symptoms in a dose-dependent manner in patients with fructose malabsorption and IBS.

Some IBS patients believe they have some form of dietary intolerance; however, tests attempting to predict food sensitivity in IBS have proven disappointing. A small study reported that an IgG antibody test was somewhat effective in determining food sensitivity in IBS patients, with patients on the elimination diet experiencing 10% greater symptom-reduction than those on a sham diet. However, more research is necessary before IgG testing can be recommended.

People with the above symptoms are commonly studied with computed tomography, or CT scan. The CT scan is very accurate (98%) in diagnosing diverticulitis. In order to extract the most information possible about the patient's condition, thin section (5 mm) transverse images are obtained through the entire abdomen and pelvis after the patient has been administered oral and intravascular contrast. Images reveal localized colon wall thickening, with inflammation extending into the fat surrounding the colon. The diagnosis of acute diverticulitis is made confidently when the involved segment contains diverticula. CT may also identify patients with more complicated diverticulitis, such as those with an associated abscess. It may even allow for radiologically guided drainage of an associated abscess, sparing a patient from immediate surgical intervention.

Other studies, such as barium enema and colonoscopy, are contraindicated in the acute phase of diverticulitis because of the risk of perforation.

The severity of diverticulitis can be radiographically graded by the Hinchey Classification.

Stable patients presenting to A&E (accident and emergency department) or ER (emergency room) with severe abdominal pain will almost always have an abdominal x-ray and/or a CT scan. These tests can provide a differential diagnosis between simple and complex pathologies. However, in the unstable patient, fluid resuscitation and a FAST-ultrasound are done first, and if the latter is positive for free fluid, straight to surgery. They may also provide evidence to the doctor whether surgical intervention is necessary.

Patients will also most likely receive a complete blood count (or full blood count in the U.K.), looking for characteristic findings such as neutrophilia in appendicitis.

Traditionally, the use of opiates or other painkillers in patients with an acute abdomen has been discouraged before the clinical examination, because these would alter the examination. However, the scientific literature does not reveal any negative results from these alterations.

The main diagnostic tools are blood tests, X-rays of the abdomen, CT scanning, and/or ultrasound. If a mass is identified, biopsy may determine the nature of the mass.

Radiological signs of bowel obstruction include bowel distension and the presence of multiple (more than six) gas-fluid levels on supine and erect abdominal radiographs.

Contrast enema or small bowel series or CT scan can be used to define the level of obstruction, whether the obstruction is partial or complete, and to help define the cause of the obstruction.

According to a meta-analysis of prospective studies by the Cochrane Collaboration, the appearance of water-soluble contrast in the cecum on an abdominal radiograph within 24 hours of oral administration predicts resolution of an adhesive small bowel obstruction with a pooled sensitivity of 97% and specificity of 96%.

Colonoscopy, small bowel investigation with ingested camera or push endoscopy, and laparoscopy are other diagnostic options.

The initial diagnostic workup for ulcerative colitis includes the following:

- A complete blood count is done to check for anemia; thrombocytosis, a high platelet count, is occasionally seen

- Electrolyte studies and renal function tests are done, as chronic diarrhea may be associated with hypokalemia, hypomagnesemia and pre-renal failure.

- Liver function tests are performed to screen for bile duct involvement: primary sclerosing cholangitis.

- X-ray

- Urinalysis

- Stool culture, to rule out parasites and infectious causes.

- Erythrocyte sedimentation rate can be measured, with an elevated sedimentation rate indicating that an inflammatory process is present.

- C-reactive protein can be measured, with an elevated level being another indication of inflammation.

- Sigmoidoscopy a type of endoscopy which can detect the presence of ulcers in the large intestine after a trial of an enema.

Although ulcerative colitis is a disease of unknown causation, inquiry should be made as to unusual factors believed to trigger the disease.

The simple clinical colitis activity index was created in 1998 and is used to assess the severity of symptoms.

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.

The diagnosis is usually confirmed by biopsies on colonoscopy. Fecal calprotectin is useful as an initial investigation, which may suggest the possibility of IBD, as this test is sensitive but not specific for IBD.

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.

There is a recent optical test, but it requires endoscopy (see Diagnosis). There are no specific blood tests for ischemic colitis. The sensitivity of tests among 73 patients were:

- The white blood cell count was more than 15,000/mm3 in 20 patients (27%)

- The serum bicarbonate level was less than 24 mmol/L in 26 patients (36%)

Plain X-rays are often normal or show non-specific findings. In a series of 73 patients, plain abdominal radiography (56%) showing colic distension in 53% or a pneumoperitoneum in 3%.

CT scans are often used in the evaluation of abdominal pain and rectal bleeding, and may suggest the diagnosis of ischemic colitis, pick up complications, or suggest an alternate diagnosis.

Endoscopic evaluation, via colonoscopy or flexible sigmoidoscopy, is the procedure of choice if the diagnosis remains unclear. Ischemic colitis has a distinctive endoscopic appearance; endoscopy can also facilitate alternate diagnoses such as infection or inflammatory bowel disease. Biopsies can be taken via endoscopy to provide more information. Visible light spectroscopy, performed using catheters placed through the 5 mm channel of the endoscope, is diagnostic (see Diagnosis).

Functional constipation is common and does not warrant diagnostic testing. Imaging and laboratory tests are typically recommended for those with alarm signs or symptoms.

The laboratory tests performed depends on the suspected underlying cause of the constipation. Tests may include CBC (complete blood count), thyroid function tests, serum calcium, serum potassium, etc.

Abdominal X-rays are generally only performed if bowel obstruction is suspected, may reveal extensive impacted fecal matter in the colon, and may confirm or rule out other causes of similar symptoms.

Colonoscopy may be performed if an abnormality in the colon like a tumor is suspected. Other tests rarely ordered include anorectal manometry, anal sphincter electromyography, and defecography.

Colonic propagating pressure wave sequences (PSs) are responsible for discrete movements of the bowel contents and are vital for normal defecation. Deficiencies in PS frequency, amplitude, and extent of propagation are all implicated in severe defecatory dysfunction (SDD). Mechanisms that can normalize these aberrant motor patterns may help rectify the problem. Recently the novel therapy of sacral nerve stimulation (SNS) has been utilized for the treatment of severe constipation.

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

Fetal and neonatal bowel obstructions are often caused by an intestinal atresia, where there is a narrowing or absence of a part of the intestine. These atresias are often discovered before birth via an ultrasound, and treated with using laparotomy after birth. If the area affected is small, then the surgeon may be able to remove the damaged portion and join the intestine back together. In instances where the narrowing is longer, or the area is damaged and cannot be used for a period of time, a temporary stoma may be placed.

In children, insussusception at the ileocecal junction and accounts for 90 percent of all cases.

There is considerable research into the causes, diagnosis and treatments for FGIDs. Diet, microbiome, genetics, neuromuscular function and immunological response all interact. Heightened mast cell activation has been proposed to be a common factor among FGIDs, contributing to visceral hypersensitivity as well as epithelial, neuromuscular, and motility dysfunction.

The best test for diagnosis of ulcerative colitis remains endoscopy. Full colonoscopy to the cecum and entry into the terminal ileum is attempted only if the diagnosis of UC is unclear. Otherwise, a flexible sigmoidoscopy is sufficient to support the diagnosis. The physician may elect to limit the extent of the exam if severe colitis is encountered to minimize the risk of perforation of the colon. Endoscopic findings in ulcerative colitis include the following:

- Loss of the vascular appearance of the colon

- Erythema (or redness of the mucosa) and friability of the mucosa

- Superficial ulceration, which may be confluent, and

- Pseudopolyps.

Ulcerative colitis is usually continuous from the rectum, with the rectum almost universally being involved. Perianal disease is rare. The degree of involvement endoscopically ranges from proctitis or inflammation of the rectum, to left sided colitis, to pancolitis, which is inflammation involving the ascending colon.

Medication (to prevent spasms) or Sphincterotomy (surgical procedure to cut the muscle) are the standard treatments for sphincter of Oddi dysfunction. One or the other may be better based on the classification of the condition.

There may be signs of septic shock. A physical examination reveals abdominal tenderness and possible loss of bowel sounds. An abdominal radiography shows colonic dilation. White blood cell count is usually elevated. Severe sepsis may present with hypothermia or leukopenia.

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.

On x-rays, gas may be visible in the abdominal cavity. Gas is easily visualized on x-ray while the patient is in an upright position. The perforation can often be visualised using computed tomography. White blood cells are often elevated.

The exact incidence of ischemic colitis is difficult to estimate, as many patients with mild ischemia may not seek medical attention. Ischemic colitis is responsible for about 1 in 2000 hospital admissions, and is seen on about 1 in 100 endoscopies. Men and women are affected equally; ischemic colitis is a disease of the elderly, with more than 90% of cases occurring in people over the age of 60.

Multiple disorders are found in patients with radiation enteropathy, so guidance including an algorithmic approach to their investigation has been developed. This includes a holistic assessment with investigations including endoscopies, breath tests and other nutritional and gastrointestinal tests. Full investigation is important as many cancer survivors of radiation therapy develop other causes for their symptoms such as colonic polyps, diverticular disease or hemorrhoids.

Other diseases may cause an increased excretion of fecal calprotectin, such as infectious diarrhea, untreated coeliac disease, necrotizing enterocolitis, intestinal cystic fibrosis and neoplastic pediatric tumor cells.

Conditions with similar symptoms as Crohn's disease includes intestinal tuberculosis, Behçet's disease, ulcerative colitis, nonsteroidal anti-inflammatory drug enteropathy, irritable bowel syndrome and coeliac disease.

Conditions with similar symptoms as ulcerative colitis includes acute self-limiting colitis, amebic colitis, schistosomiasis, Crohn's disease, colon cancer, irritable bowel syndrome, intestinal tuberculosis and nonsteroidal anti-inflammatory drug enteropathy.