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

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

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.

IBS can be classified as either diarrhea-predominant (IBS-D), constipation-predominant (IBS-C), or with alternating stool pattern (IBS-A) or pain-predominant. In some individuals, IBS may have an acute onset and develop after an infectious illness characterized by two or more of: fever, vomiting, diarrhea, or positive stool culture. This postinfective syndrome has consequently been termed "postinfectious IBS" (IBS-PI).

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.

Constipation is a symptom, not a disease. Most commonly, constipation is thought of as infrequent bowel movements, usually less than 3 stools per week. However, people may have other complaints as well including:

- Straining with bowel movements

- Excessive time needed to pass a bowel movement

- Hard stools

- Pain with bowel movements secondary to straining

- Abdominal pain

- Abdominal bloating.

- the sensation of incomplete bowel evacuation.

The Rome Criteria are a set of symptoms that help standardize the diagnosis of constipation in various age groups. These criteria help physicians to better define constipation in a standardized manner.

In most cases, the clinical history is of limited use in distinguishing between organic causes and functional dyspepsia. A large systematic review of the literature was recently performed to evaluate the effectiveness of diagnosing organic dyspepsia by clinical opinion versus computer models in patients referred for upper endoscopy. The computer models were based on patient demographics, risk factors, historical items, and symptoms. The study showed that neither clinical impression nor computer models were able to adequately distinguish organic from functional disease.

In a recent study, patients with peptic ulcer disease were compared with patients with functional dyspepsia in an age and sex-matched study. Although the functional dyspepsia group reported more upper abdominal fullness, nausea, and overall greater distress and anxiety, almost all the same symptoms were seen in both groups.

Therefore, it is the clinician’s challenging task to separate patients who may have an organic disorder, and thus warrant further diagnostic testing, from patients who have functional dyspepsia, who are given empiric symptomatic treatment.The workup should be targeted to identify or rule out specific causes. Traditionally, people at high-risk have been identified by “alarm” features. However, the utility of these features in identifying the presence of upper cancer of the esophagus or stomach has been debated. A meta analysis looking at the sensitivity and specificity of alarm features found a range of 0–83% and 40–98%, respectively. However, there was high heterogeneity between studies.

The physical examination may elicit abdominal tenderness, but this finding is nonspecific. A positive Carnett sign, or focal tenderness that increases with abdominal wall contraction and palpation, suggests an etiology involving the abdominal wall musculature. Cutaneous dermatomal distribution of pain may suggest a thoracic polyradiculopathy. Thump tenderness over the right upper quadrant may suggest chronic cholecystitis.

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.

Constipation refers to bowel movements that are infrequent or hard to pass. The stool is often hard and dry. Other symptoms may include abdominal pain, bloating, and feeling as if one has not completely passed the bowel movement. Complications from constipation may include hemorrhoids, anal fissure or fecal impaction. The normal frequency of bowel movements in adults is between three per day and three per week. Babies often have three to four bowel movements per day while young children typically have two to three per day.

Constipation has many causes. Common causes include slow movement of stool within the colon, irritable bowel syndrome, and pelvic floor disorders. Underlying associated diseases include hypothyroidism, diabetes, Parkinson's disease, celiac disease, non-celiac gluten sensitivity, colon cancer, diverticulitis, and inflammatory bowel disease. Medications associated with constipation include opioids, certain antacids, calcium channel blockers, and anticholinergics. Of those taking opioids about 90% develop constipation. Constipation is more concerning when there is weight loss or anemia, blood is present in the stool, there is a history of inflammatory bowel disease or colon cancer in a person's family, or it is of new onset in someone who is older.

Treatment of constipation depends on the underlying cause and the duration that it has been present. Measures that may help include drinking enough fluids, eating more fiber, and exercise. If this is not effective, laxatives of the bulk forming agent, osmotic agent, stool softener, or lubricant type may be recommended. Stimulant laxatives are generally reserved for when other types are not effective. Other treatments may include biofeedback or in rare cases surgery.

In the general population rates of constipation are 2–30 percent. Among elderly people living in a care home the rate of constipation is 50–75 percent. People spend, in the United States, more than on medications for constipation a year.

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

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.

The small and large intestines may be affected by infectious, autoimmune, and physiological states. Inflammation of the intestines is called enterocolitis, which may lead to diarrhoea.

Acute conditions affecting the bowels include infectious diarrhoea and mesenteric ischaemia. Causes of constipation may include faecal impaction and bowel obstruction, which may in turn be caused by ileus, intussusception, volvulus. Inflammatory bowel disease is a condition of unknown aetiology, classified as either Crohn's disease or ulcerative colitis, that can affect the intestines and other parts of the gastrointestinal tract. Other causes of illness include intestinal pseudoobstruction, and necrotizing enterocolitis.

Diseases of the intestine may cause vomiting, diarrhoea or constipation, and altered stool, such as with blood in stool. Colonoscopy may be used to examine the large intestine, and a person's stool may be sent for culture and microscopy. Infectious disease may be treated with targeted antibiotics, and inflammatory bowel disease with immunosuppression. Surgery may also be used to treat some causes of bowel obstruction.

The normal thickness of the small intestinal wall is 3–5 mm, and 1–5 mm in the large intestine. Focal, irregular and asymmetrical gastrointestinal wall thickening on CT scan suggests a malignancy. Segmental or diffuse gastrointestinal wall thickening is most often due to ischemic, inflammatory or infectious disease.

People may vomit or retch six to twelve times an hour, and an episode may last from a few hours to well over three weeks, and in some cases months, with a median episode duration of 41 hours. Acid, bile and (if the vomiting is severe) blood may be vomited. Some sufferers will ingest water to reduce the irritation of bile and acid on the esophagus during emesis. Between episodes the sufferer is usually normal and healthy otherwise but can be in a weak state of fatigue or suffer from muscle pain. In approximately half of cases the attacks, or episodes, occur in a time-related manner. Each attack is stereotypical; that is, in any given individual, the timing, frequency and severity of attacks is similar.

Episodes may happen every few days, every few weeks or every few months. For some there is not a pattern in time that can be recognized. Some sufferers have a warning of an attack. They may experience a prodrome, usually intense nausea and pallor, heightened sensitivity, especially to light, though sensitivity to smell, sound, pressure, and temperature, as well as oncoming muscle pain and fatigue, are also reported by some patients. The majority of sufferers can identify triggers that may precipitate an attack. The most common are various foods, infections (such as colds), menstruation, extreme physical exertion, lack of sleep, and psychological stresses both positive and negative.

A sufferer may also be light-sensitive (photophobic) during an attack, as well as sound-sensitive (phonophobic) and, less frequently, temperature- or pressure-sensitive. Some sufferers also have a strong urge to bathe in warm or cold water. Some sufferers report that they experience a restless sensation or stinging pain along the spine, hands, and feet followed by weakness in both legs. Some of these symptoms may be due to dehydration rather than the underlying cause of CVS.

AEN has never been recorded as a one symptom disorder, but instead present by multiple symptoms. The symptoms vary from the severity of the disorder. The most classic sign of AEN is the dark pigmentation of esophageal mucosa in an upper endoscopy, usually viewed as an ulcer or as an infectious disease. Necrosis can be found mostly between the three distals of the esophagus, but stops abruptly at the gastroesophageal junction. The basic and most common symptoms reported are blood in stool and blood in vomiting. Upper gastrointestinal bleeding then is reported, and is very commonly represented in elderly patients. Black or bloody stools and hematemesis account for over three quarters of the case presentations. Abdominal pain, nausea, vomiting, and unstable vital signs are common. A cardiovascular event (such as a heart attack) was reported in ten percent of the total known cases.

While the number and severity of symptoms varies among individuals, repetitive regurgitation of undigested food (known as rumination) after the start of a meal is always present. In some individuals, the regurgitation is small, occurring over a long period of time following ingestion, and can be rechewed and swallowed. In others, the amount can be bilious and short lasting, and must be expelled.

While some only experience symptoms following some meals, most experience episodes following any ingestion, from a single bite to a massive feast. However, some long-term patients will find a select couple of food or drink items that do not trigger a response.

Unlike typical vomiting, the regurgitation is typically described as effortless and unforced. There is seldom nausea preceding the expulsion, and the undigested food lacks the bitter taste and odour of stomach acid and bile.

Symptoms can begin to manifest at any point from the ingestion of the meal to 120 minutes thereafter. However, the more common range is between 30 seconds to 1 hour after the completion of a meal. Symptoms tend to cease when the ruminated contents become acidic.

Abdominal pain (38.1%), lack of fecal production or constipation (21.1%), nausea (17.0%), diarrhea (8.2%), bloating (4.1%), and dental decay (3.4%) are also described as common symptoms in day-to-day life. These symptoms are not necessarily prevalent during regurgitation episodes, and can happen at any time. Weight loss is often observed (42.2%) at an average loss of 9.6 kilograms, and is more common in cases where the disorder has gone undiagnosed for a longer period of time, though this may be expected of the nutrition deficiencies that often accompany the disorder as a consequence of its symptoms. Depression has also been linked with rumination syndrome, though its effects on rumination syndrome are unknown.

Acid erosion of the teeth can be a feature of rumination, as can halitosis (bad breath).

Rumination syndrome in adults is a complicated disorder whose symptoms can mimic those of several other gastroesophogeal disorders and diseases. Bulimia nervosa and gastroparesis are especially prevalent among the misdiagnoses of rumination.

Bulimia nervosa, among adults and especially adolescents, is by far the most common misdiagnosis patients will hear during their experiences with rumination syndrome. This is due to the similarities in symptoms to an outside observer—"vomiting" following food intake—which, in long-term patients, may include ingesting copious amounts to offset malnutrition, and a lack of willingness to expose their condition and its symptoms. While it has been suggested that there is a connection between rumination and bulimia, unlike bulimia, rumination is not self-inflicted. Adults and adolescents with rumination syndrome are generally well aware of their gradually increasing malnutrition, but are unable to control the reflex. In contrast, those with bulimia intentionally induce vomiting, and seldom re-swallow food.

Gastroparesis is another common misdiagnosis. Like rumination syndrome, patients with gastroparesis often bring up food following the ingestion of a meal. Unlike rumination, gastroparesis causes vomiting (in contrast to regurgitation) of food, which is not being digested further, from the stomach. This vomiting occurs several hours after a meal is ingested, preceded by nausea and retching, and has the bitter or sour taste typical of vomit.

There are established criteria to aid in diagnosis of CVS; essential criteria are:

1. A history of three or more periods of intense, acute nausea and unremitting vomiting, as well as pain in some cases, lasting hours to days and even weeks or months

2. Intervening symptom-free or reduced-symptom intervals, lasting weeks to months

3. There are repeated cycles of periods (of varying duration) with intense/acute nausea, with or without vomiting, with or without severe pain, followed by periods of reduced symptoms, followed by gradual increase in CVS symptoms until it peaks (peak intensity is generally relative to cycle intensity).

4. There are differences between early-onset CVS (babies & children) and late onset CVS (adult).

5. Exclusion of metabolic, gastrointestinal, or central nervous system structural or biochemical disease, e.g., individuals with specific physical causes (such as intestinal malrotation)

EE is rarely symptomatic and is considered a subclinical condition. However, adults may have mild symptoms or malabsorption such as altered stool consistency, increased stool frequency and weight loss.

Proximal enteritis, also known as anterior enteritis or duodenitis-proximal jejunitis (DPJ), is inflammation of the duodenum and upper jejunum. It produces a functional stasis of the affected intestine (ileus) and hypersecretion of fluid into the lumen of that intestine. This leads to large volumes of gastric reflux, dehydration, low blood pressure, and potentially shock. Although the exact cause is not yet definitively known, proximal enteritis requires considerable supportive care.

Bile acid malabsorption, known also as bile acid diarrhea, is a cause of several gut-related problems, the main one being chronic diarrhea. It has also been called bile acid-induced diarrhea, cholerheic or choleretic enteropathy and bile salt malabsorption. It can result from malabsorption secondary to gastrointestinal disease, or be a primary disorder, associated with excessive bile acid production. Treatment with bile acid sequestrants is often effective.

A gastrojejunocolic fistula is a disorder of the human gastrointestinal tract. It may form between the transverse colon and the upper jejunum after a Billroth II surgical procedure. (The Billroth procedure attaches the jejunum to the remainder of the stomach). Fecal matter thereby passes improperly from the colon to the stomach, and causes halitosis.

Patients may present with diarrhea, weight loss and halitosis as a result of fecal matter passing through the fistula from the colon into the stomach.

DPJ is most commonly seen in the Southeastern US, although cases have been reported throughout the United States and Canada, as well as sporadically in the United Kingdom and Europe. Horses in the Southeastern US tend to have a more severe form of the disease relative to other locations. Age, breed, and gender appear to have no effect on disease prevalence.

Acute esophageal necrosis can only be diagnosed by an upper gastrointestinal endoscopy.

Functional disorders of the gallbladder, bile duct and pancreas have been defined and classified by the Rome criteria for functional gastrointestinal disorders. The criteria outline three variants of functional disorders of the gallbladder, bile duct and pancreas, termed "functional gallbladder disorder", "functional biliary sphincter of Oddi disorder" and "functional pancreatic sphincter of Oddi disorder". All of the following criteria need to be met for as part of the definition of a functional disorder of the gallbladder:

- the pain must be located in the upper part of the abdomen and/or the right upper quadrant of the abdomen

- episodes of pain must last at least 30 minutes

- the symptoms must be recurrent, and occur at differing intervals

- the pain must incrementally increase to a "steady level"

- the pain must be severe enough the patient's daily activities are affected, or that the patient must attend the emergency department

- the pain must not be relieved by any of bowel movements, change in posture, or antacids; and,

- other structural disorders that could explain the symptoms must be excluded.

Bile acid malabsorption was first recognized in patients with ileal disease. When other causes were recognized, and an idiopathic, primary form described, a classification into three types was proposed:

- Type 1: Bile acid malabsorption, secondary to ileal resection, or ileal inflammation (e.g. in Crohn's disease)

- Type 2: Idiopathic bile acid malabsorption, Primary bile acid diarrhea

- Type 3: Secondary to various gastrointestinal diseases including cholecystectomy, vagotomy, small intestinal bacterial overgrowth, radiation enteropathy, celiac disease, chronic pancreatitis, etc.