The symptoms of short bowel syndrome can include:

- Abdominal pain

- Diarrhea and steatorrhea (oily, bulky stool, which can be malodorous)

- Fluid depletion

- Weight loss and malnutrition

- Fatigue

Persons with short bowel syndrome may have complications caused by malabsorption of vitamins and minerals, such as deficiencies in vitamins A, D, E, K, B (folic acid), and B, calcium, magnesium, iron, and zinc. These may appear as anemia, hyperkeratosis (scaling of the skin), easy bruising, muscle spasms, poor blood clotting, and bone pain.

Intestinal failure is decreased intestinal function such that nutrients, water, and electrolytes are not sufficiently absorbed. Short bowel syndrome is when there is less than of working bowel and is the most common cause of intestinal failure.

Terms such as "functional colonic disease" (or "functional bowel disorder") refer in medicine to a group of bowel disorders which are characterised by chronic abdominal complaints without a structural or biochemical cause that could explain symptoms. Other "functional" disorders relate to other aspects of the process of digestion.

The consensus review process of meetings and publications organised by the Rome Foundation, known as the Rome process, has helped to define the functional gastrointestinal disorders. Successively, the Rome I, Rome II, Rome III and Rome IV proposed consensual classification system and terminology, as recommended by the Rome Coordinating Committee. These now include classifications appropriate for adults, children and neonates / toddlers.

The current Rome IV classification, published in 2016, is as follows:

A. Esophageal Disorders

- A1. Functional chest pain

- A2. Functional heartburn

- A3. Reflux hypersensitivity

- A4. Globus

- A5. Functional dysphagia

B. Gastroduodenal Disorders

- B1. Functional dyspepsia

- B1a. Postprandial distress syndrome (PDS)

- B1b. Epigastric pain syndrome (EPS)

- B2. Belching disorders

- B2a. Excessive supragastric belching

- B2b. Excessive gastric belching

- B3. Nausea and vomiting disorders

- B3a. Chronic nausea vomiting syndrome (CNVS}

- B3b. Cyclic vomiting syndrome (CVS)

- B3c. Cannabinoid hyperemesis syndrome (CHS)

- B4. Rumination syndrome

C. Bowel Disorders

- C1. Irritable bowel syndrome (IBS)

- IBS with predominant constipation (IBS-C)

- IBS with predominant diarrhea (IBS-D)

- IBS with mixed bowel habits (IBS-M)

- IBS unclassified (IBS-U)

- C2. Functional constipation

- C3. Functional diarrhea

- C4. Functional abdominal bloating/distension

- C5. Unspecified functional bowel disorder

- C6. Opioid-induced constipation

D. Centrally Mediated Disorders of Gastrointestinal Pain

- D1. Centrally mediated abdominal pain syndrome (CAPS)

- D2. Narcotic bowel syndrome (NBS)/ Opioid-induced GI hyperalgesia

E. Gallbladder and Sphincter of Oddi disorders

- E1. Biliary pain

- E1a. Functional gallbladder disorder

- E1b. Functional biliary sphincter of Oddi disorder

- E2. Functional pancreatic sphincter of Oddi disorder

F. Anorectal Disorders

- F1. Fecal incontinence

- F2. Functional anorectal pain

- F2a. Levator ani syndrome

- F2b. Unspecified functional anorectal pain

- F2c. Proctalgia fugax

- F3. Functional defecation disorders

- F3a. Inadequate defecatory propulsion

- F3b. Dyssynergic defecation

G. Childhood Functional GI Disorders: Neonate/Toddler

- G1. Infant regurgitation

- G2. Rumination syndrome

- G3. Cyclic vomiting syndrome (CVS)

- G4. Infant colic

- G5. Functional diarrhea

- G6. Infant dyschezia

- G7. Functional constipation

H. Childhood Functional GI Disorders: Child/Adolescent

- H1. Functional nausea and vomiting disorders

- H1a. Cyclic vomiting syndrome (CVS)

- H1b. Functional nausea and functional vomiting

- H1b1. Functional nausea

- H1b2. Functional vomiting

- H1c. Rumination syndrome

- H1d. Aerophagia

- H2. Functional abdominal pain disorders

- H2a. Functional dyspepsia

- H2a1. Postprandial distress syndrome

- H2a2. Epigastric pain syndrome

- H2b. Irritable bowel syndrome (IBS)

- H2c. Abdominal migraine

- H2d. Functional abdominal pain ‒ NOS

- H3. Functional defecation disorders

- H3a. Functional constipation

- H3b. Nonretentive fecal incontinence

The small intestine consists of the duodenum, jejunum and ileum. Inflammation of the small intestine is called enteritis, which if localised to just part is called duodenitis, jejunitis and ileitis, respectively. Peptic ulcers are also common in the duodenum.

Chronic diseases of malabsorption may affect the small intestine, including the autoimmune coeliac disease, infective Tropical sprue, and congenital or surgical short bowel syndrome. Other rarer diseases affecting the small intestine include Curling's ulcer, blind loop syndrome, Milroy disease and Whipple's disease. Tumours of the small intestine include gastrointestinal stromal tumours, lipomas, hamartomas and carcinoid syndromes.

Diseases of the small intestine may present with symptoms such as diarrhoea, malnutrition, fatigue and weight loss. Investigations pursued may include blood tests to monitor nutrition, such as iron levels, folate and calcium, endoscopy and biopsy of the duodenum, and barium swallow. Treatments may include renutrition, and antibiotics for infections.

External signs and symptoms are constipation of very long duration, abdominal bloating, abdominal tenderness and tympany, abdominal pain, palpation of hard fecal masses and, in toxic megacolon, fever, low blood potassium, tachycardia and shock. Stercoral ulcers are sometimes observed in chronic megacolon, which may lead to perforation of the intestinal wall in approximately 3% of the cases, leading to sepsis and risk of death.

In about 50-70% of patients with dyspepsia, no definite organic cause can be determined. In this case, dyspepsia is referred to as non-ulcer dyspepsia and its diagnosis is established by the presence of epigastralgia for at least 6 months, in the absence of any other cause explaining the symptoms.

Functional gastrointestinal disorders are very common. Globally, irritable bowel syndrome and functional dyspepsia alone may affect 16–26% of the population.

Diseases that affect the large intestine may affect it in whole or in part. Appendicitis is one such disease, caused by inflammation of the appendix. Generalised inflammation of the large intestine is referred to as colitis, which when caused be the bacteria "Clostridium difficile" is referred to as pseudomembranous colitis. Diverticulitis is a common cause of abdominal pain resulting from outpouchings that particularly affects the colon. Functional colonic diseases refer to disorders without a known cause, and include irritable bowel syndrome and intestinal pseudoobstruction. Constipation may result from lifestyle factors, impaction of a rigid stool in the rectum, or in neonates, Hirschprung's disease.

Diseases affecting the large intestine may cause blood to be passed with stool, may cause constipation, or may result in abdominal pain or a fever. Tests that specifically examine the function of the large intestine include barium swallows, abdominal x-rays, and colonoscopy.

In spite of Crohn's and UC being very different diseases, both may present with any of the following symptoms: abdominal pain, vomiting, diarrhea, rectal bleeding, severe internal cramps/muscle spasms in the region of the pelvis and weight loss. Anemia is the most prevalent extraintestinal complication of inflammatory bowel disease. Associated complaints or diseases include arthritis, pyoderma gangrenosum, primary sclerosing cholangitis, and non-thyroidal illness syndrome (NTIS). Associations with deep vein thrombosis (DVT) and bronchiolitis obliterans organizing pneumonia (BOOP) have also been reported. Diagnosis is generally by assessment of inflammatory markers in stool followed by colonoscopy with biopsy of pathological lesions.

The primary symptoms of IBS are abdominal pain or discomfort in association with frequent diarrhea or constipation and a change in bowel habits. Symptoms usually are experienced as acute attacks that subside within one day, but recurrent attacks are likely. There may also be urgency for bowel movements, a feeling of incomplete evacuation (tenesmus), bloating, or abdominal distension. In some cases, the symptoms are relieved by bowel movements. People with IBS, more commonly than others, have gastroesophageal reflux, symptoms relating to the genitourinary system, chronic fatigue syndrome, fibromyalgia, headache, backache, and psychiatric symptoms such as depression and anxiety. About a third of men and women who have IBS also report sexual dysfunction typically in the form of a reduction in libido.

Inflammatory bowel disease (IBD) is a group of inflammatory conditions of the colon and small intestine. Crohn's disease and ulcerative colitis are the principal types of inflammatory bowel disease. It is important to note that not only does Crohn's disease affect the small intestine and large intestine, it can also affect the mouth, esophagus, stomach and the anus whereas ulcerative colitis primarily affects the colon and the rectum.

Symptoms of ileus include, but are not limited to:

- moderate, diffuse abdominal discomfort

- constipation

- abdominal distension

- nausea/vomiting, especially after meals

- vomiting of bilious fluid

- lack of bowel movement and/or flatulence

- excessive belching

Megacolon is an abnormal dilation of the colon (also called the large intestine). The dilation is often accompanied by a paralysis of the peristaltic movements of the bowel. In more extreme cases, the feces consolidate into hard masses inside the colon, called fecalomas (literally, "fecal tumor"), which can require surgery to be removed.

A human colon is considered abnormally enlarged if it has a diameter greater than 12 cm in the cecum (it is usually less than 9 cm), greater than 6.5 cm in the rectosigmoid region and greater than 8 cm for the ascending colon. The transverse colon is usually less than 6 cm in diameter.

A megacolon can be either acute or chronic. It can also be classified according to cause.

Depending on the level of obstruction, bowel obstruction can present with abdominal pain, swollen abdomen, abdominal distension, vomiting, fecal vomiting, and constipation.

Bowel obstruction may be complicated by dehydration and electrolyte abnormalities due to vomiting; respiratory compromise from pressure on the diaphragm by a distended abdomen, or aspiration of vomitus; bowel ischemia or perforation from prolonged distension or pressure from a foreign body.

In small bowel obstruction, the pain tends to be colicky (cramping and intermittent) in nature, with spasms lasting a few minutes. The pain tends to be central and mid-abdominal. Vomiting may occur before constipation.

In large bowel obstruction, the pain is felt lower in the abdomen and the spasms last longer. Constipation occurs earlier and vomiting may be less prominent. Proximal obstruction of the large bowel may present as small bowel obstruction.

Several medical conditions, or comorbidities, appear with greater frequency in patients diagnosed with IBS.

- Neurological/psychiatric: A study of 97,593 individuals with IBS identified comorbidities such as headache, fibromyalgia, and depression. IBS occurs in 51% of chronic fatigue syndrome patients and 49% of fibromyalgia patients, and psychiatric disorders occur in 94% of IBS patients.

- Inflammatory bowel disease: IBS may be a type of low-grade inflammatory bowel disease. Researchers have suggested IBS and IBD are interrelated diseases, noting that patients with IBD experience IBS-like symptoms when their IBD is in remission. A three-year study found that patients diagnosed with IBS were 16.3 times more likely to be diagnosed with IBD during the study period. Serum markers associated with inflammation have also been found in patients with IBS.

- Abdominal surgery: IBS patients were at increased risk of having unnecessary gall bladder removal surgery not due to an increased risk of gallstones, but rather to abdominal pain, awareness of having gallstones, and inappropriate surgical indications. These patients also are 87% more likely to undergo abdominal and pelvic surgery and three times more likely to undergo gallbladder surgery. Also, IBS patients were twice as likely to undergo hysterectomy.

- Endometriosis: One study reported a statistically significant link between migraine headaches, IBS, and endometriosis.

- Other chronic disorders: Interstitial cystitis may be associated with other chronic pain syndromes, such as irritable bowel syndrome and fibromyalgia. The connection between these syndromes is unknown.

Decreased propulsive ability may be broadly classified as caused either by bowel obstruction or intestinal atony or paralysis. However, instances with symptoms and signs of a bowel obstruction occur, but with the absence of a mechanical obstruction, mainly in acute colonic pseudo-obstruction, Ogilvie's syndrome.

This is the most common cause of chronic "dyspepsia". More than 70% of people have no obvious organic cause for their symptoms after evaluation. Symptoms may arise from a complex interaction of increased visceral afferent sensitivity, gastric delayed emptying (gastroparesis) or impaired accommodation to food. Anxiety is also associated with functional dyspepsia. In some people, it appears before the onset of gut symptoms; in other cases, anxiety develops after onset of the disorder, which suggests that a gut-driven brain disorder may be a possible cause. Although benign, these symptoms may be chronic and difficult to treat.

Wheat and dietary fats can lead to dyspepsia and their reduction or withdrawal may improve symptoms.

Causes of small bowel obstruction include:

- Adhesions from previous abdominal surgery (most common cause)

- Barbed sutures.

- Pseudoobstruction

- Hernias containing bowel

- Crohn's disease causing adhesions or inflammatory strictures

- Neoplasms, benign or malignant

- Intussusception

- Volvulus

- Superior mesenteric artery syndrome, a compression of the duodenum by the superior mesenteric artery and the abdominal aorta

- Ischemic strictures

- Foreign bodies (e.g. gallstones in gallstone ileus, swallowed objects)

- Intestinal atresia

After abdominal surgery, the incidence of small bowel obstruction from any cause is 9%. In those where the cause of the obstruction was clear, adhesions are the single most common cause (more than half).

Usually the patient has abdominal distention, pain and altered bowel movements. There may also be nausea and vomiting.

Bowel infarction results from restricted blood supply to the bowel, most often due to bowel obstruction or occlusion of one of the mesenteric arteries.

Bowel obstruction is most often caused by intestinal adhesions, which frequently form after abdominal surgeries, or by chronic infections such as diverticulitis, hepatitis, and inflammatory bowel disease. The condition is difficult to diagnose properly, as the symptoms may resemble those of other bowel disorders.

Patients who have undergone extensive resection of the small bowel may develop malabsorption, indicating the need for dietary supplements.

Volvulus is a rare but life-threatening cause of bowel infarction which requires immediate medical attention. Central abdominal pain which is resistant to narcotic analgesia may be an indication of bowel infarction.

Many people with Crohn's disease have symptoms for years before the diagnosis. The usual onset is between 15 and 30 years of age, but can occur at any age. Because of the 'patchy' nature of the gastrointestinal disease and the depth of tissue involvement, initial symptoms can be more subtle than those of ulcerative colitis. People with Crohn's disease experience chronic recurring periods of flare-ups and remission.

Abdominal pain may be the initial symptom of Crohn's disease usually in the lower right area. It is often accompanied by diarrhea, especially in those who have had surgery. The diarrhea may or may not be bloody. The nature of the diarrhea in Crohn's disease depends on the part of the small intestine or colon involved. Ileitis typically results in large-volume, watery feces. Colitis may result in a smaller volume of feces of higher frequency. Fecal consistency may range from solid to watery. In severe cases, an individual may have more than 20 bowel movements per day and may need to awaken at night to defecate. Visible bleeding in the feces is less common in Crohn's disease than in ulcerative colitis, but may be seen in the setting of Crohn's colitis. Bloody bowel movements typically come and go, and may be bright or dark red in color. In the setting of severe Crohn's colitis, bleeding may be copious. Flatulence and bloating may also add to the intestinal discomfort.

Symptoms caused by intestinal stenosis are also common in Crohn's disease. Abdominal pain is often most severe in areas of the bowel with stenoses. Persistent vomiting and nausea may indicate stenosis from small bowel obstruction or disease involving the stomach, pylorus, or duodenum. Although the association is greater in the context of ulcerative colitis, Crohn's disease may also be associated with primary sclerosing cholangitis, a type of inflammation of the bile ducts.

Perianal discomfort may also be prominent in Crohn's disease. Itchiness or pain around the anus may be suggestive of inflammation, fistulization or abscess around the anal area or anal fissure. Perianal skin tags are also common in Crohn's disease and may appear with or without the presence of colorectal polyps. Fecal incontinence may accompany perianal Crohn's disease. At the opposite end of the gastrointestinal tract, the mouth may be affected by recurrent sores (aphthous ulcers). Rarely, the esophagus, and stomach may be involved in Crohn's disease. These can cause symptoms including difficulty swallowing (dysphagia), upper abdominal pain, and vomiting.

Ogilvie syndrome is the acute dilation of the colon in the absence of any mechanical obstruction in severely ill patients.

Colonic pseudo-obstruction is characterized by massive dilatation of the cecum (diameter > 10 cm) and right colon on abdominal X-ray. It is a type of megacolon, sometimes referred to as "acute megacolon", to distinguish it from toxic megacolon.

The condition carries the name of the British surgeon Sir (1887–1971), who first reported it in 1948.

Sclerosing mesenteritis may present with no or nearly no signs or symptoms, but many people have chronic and severe pain in the abdomen as the most common chief complaint. Other people have chronic problems with bowel movements, resulting in diarrhea, bloating, gas, and cramping which can range from severe to mild.

The disorder is identified by histopathology showing fat necrosis, fibrosis and chronic inflammation of the small intestine. Examination of the mesentery may indicate a solitary mass, but diffuse mesentery thickening is common.

It often mimics other abdominal diseases such as pancreatic or disseminated cancer. CT scanning is important for making the initial diagnosis.

Crohn's disease, like many other chronic, inflammatory diseases, can cause a variety of systemic symptoms. Among children, growth failure is common. Many children are first diagnosed with Crohn's disease based on inability to maintain growth. As it may manifest at the time of the growth spurt in puberty, up to 30% of children with Crohn's disease may have retardation of growth. Fever may also be present, though fevers greater than 38.5 °C (101.3 °F) are uncommon unless there is a complication such as an abscess. Among older individuals, Crohn's disease may manifest as weight loss, usually related to decreased food intake, since individuals with intestinal symptoms from Crohn's disease often feel better when they do not eat and might lose their appetite. People with extensive small intestine disease may also have malabsorption of carbohydrates or lipids, which can further exacerbate weight loss.

Bacterial overgrowth can cause a variety of symptoms, many of which are also found in other conditions, making the diagnosis challenging at times. Many of the symptoms are due to malabsorption of nutrients due to the effects of bacteria which either metabolize nutrients or cause inflammation of the small bowel, impairing absorption. The symptoms of bacterial overgrowth include nausea, flatus, constipation, bloating, abdominal distension, abdominal pain or discomfort, diarrhea, fatigue, and weakness. SIBO also causes an increased permeability of the small intestine. Some patients may lose weight. Children with bacterial overgrowth may develop malnutrition and have difficulty attaining proper growth. Steatorrhea, a sticky type of diarrhea where fats are not properly absorbed and spill into the stool, may also occur.

Patients with bacterial overgrowth that is longstanding can develop complications of their illness as a result of malabsorption of nutrients. Anemia may occur from a variety of mechanisms, as many of the nutrients involved in production of red blood cells are absorbed in the affected small bowel. Iron is absorbed in the more proximal parts of the small bowel, the duodenum and jejunum, and patients with malabsorption of iron can develop a microcytic anemia, with small red blood cells. Vitamin B is absorbed in the last part of the small bowel, the ileum, and patients who malabsorb vitamin B can develop a megaloblastic anemia with large red blood cells.

In older adults, small bowel bacterial overgrowth is associated with a higher frequency of diarrhea, a lower body mass index, and a significantly lower serum albumin concentration.