People who develop microscopic colitis are characteristically, though not exclusively, middle-aged females. The average age of diagnosis is 65 but 25% of cases are diagnosed below the age of 45. Patients have a history of non-bloody watery diarrhoea, which may be profuse. Patients may also experience abdominal pain, fecal incontinence, and weight loss. Microscopic colitis is the diagnosis in around 10% of cases investigated for chronic non-bloody diarrhea.

Colonoscopic appearances are normal or near normal. As the changes are often patchy, an examination limited to the rectum may miss cases of microscopic colitis, and so a full colonoscopy is necessary. Multiple colonic biopsies are taken in order to make the diagnosis. Histological features of colonic biopsies indicating microscopic colitis are: greater than 20 intraepithelial lymphocytes per 100 epithelial cells and, additionally, 10-20 μm of a thickened subepithelial collagen band in collagenous colitis. Inflammation of the lamina propria, with mainly mononuclear cells, may be observed in collagenous colitis.

Differential diagnoses, which should be ruled out, include celiac disease, Crohn's disease, ulcerative colitis and infectious colitis.

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.

Before a diagnosis of toddler's diarrhea is made, the following conditions should be ruled out:

- Celiac sprue (wheat gluten intolerance)

- Cystic fibrosis

- Sugar malabsorption

- Food allergy

Microscopic colitis refers to two related medical conditions which cause diarrhea: collagenous colitis and lymphocytic colitis. Both conditions are characterized by the presence of chronic non-bloody watery diarrhea, normal appearances on colonoscopy and characteristic histopathology findings of inflammatory cells.

Microscopic colitis causes chronic watery diarrhea with greater than 10 bowel movements per day. Some patients report nocturnal diarrhea, abdominal pain, urgency, fecal incontinence, fatigue, dehydration and weight loss. Patients report a significantly diminished quality of life.

The classic symptoms of coeliac disease include pale, loose, and greasy stool (steatorrhoea) and weight loss or failure to gain weight. More common symptoms are subtle or primarily occur in organs other than the bowel itself. It is also possible to have coeliac disease without any classic symptoms whatsoever. This represents at least 43% of the cases in children. Many adults with subtle disease only have fatigue or anaemia.

On colonoscopy, the mucosa of the colon typically looks normal, but biopsies of affected tissue usually show deposition of collagen in the lamina propria, which is the area of connective tissue between colonic glands. Radiological tests, such as a barium enema are also typically normal.

The illness usually starts with an attack of acute diarrhoea, fever and malaise following which, after a variable period, the patient settles into the chronic phase of diarrhoea, steatorrhoea, weight loss, anorexia, malaise, and nutritional deficiencies.

The symptoms of tropical sprue are:

- Diarrhoea

- Steatorrhoea or fatty stool (often foul-smelling and whitish in colour)

- Indigestion

- Cramps

- Weight loss and malnutrition

- Fatigue

Left untreated, nutrient and vitamin deficiencies may develop in patients with tropical sprue. These deficiencies may have these symptoms:

- Vitamin A deficiency: hyperkeratosis or skin scales

- Vitamin B and folic acid deficiencies: anaemia

- Vitamin D and calcium deficiencies: spasm, bone pain, numbness, and tingling sensation

- Vitamin K deficiency: bruises

Chronic diarrhea of infancy, also called toddler's diarrhea, is a common condition typically affecting children between ages 6–30 months, usually resolving by age 4. Symptoms include multiple loose bowel movements per day, sometimes with undigested food visible; normal growth with no evidence of malnutrition; and no evidence blood in the stool or infection. The condition may be related to irritable bowel syndrome.

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.

The diarrhoea that is characteristic of coeliac disease is (chronic) pale, of large volume, and abnormally bad smelling. Abdominal pain and cramping, bloatedness with abdominal distension (thought to be due to fermentative production of bowel gas), and mouth ulcers may be present. As the bowel becomes more damaged, a degree of lactose intolerance may develop. Frequently, the symptoms are ascribed to irritable bowel syndrome (IBS), only later to be recognised as coeliac disease; a small proportion of people with symptoms of IBS have underlying coeliac disease, and screening for coeliac disease is recommended for those with IBS symptoms.

Coeliac disease leads to an increased risk of both adenocarcinoma and lymphoma of the small bowel (enteropathy-associated T-cell lymphoma (EATL) or other non-Hodgkin's lymphomas). This risk is also higher in first-degree relatives such as siblings, parents, and children. Whether or not a gluten-free diet brings this risk back to baseline is not clear. Long-standing and untreated disease may lead to other complications, such as ulcerative jejunitis (ulcer formation of the small bowel) and stricturing (narrowing as a result of scarring with obstruction of the bowel).

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.

Small intestine bacterial overgrowth (SIBO), also termed bacterial overgrowths, or small bowel bacterial overgrowth syndrome (SBBOS), is a disorder of excessive bacterial growth in the small intestine. Unlike the colon (or large bowel), which is rich with bacteria, the small bowel usually has fewer than 10,000 organisms per millilitre. Patients with bacterial overgrowth typically develop symptoms including nausea, bloating, vomiting, diarrhea, malnutrition, weight loss and malabsorption, which is caused by a number of mechanisms.

The diagnosis of bacterial overgrowth is made by a number of techniques, with the gold standard being an aspirate from the jejunum that grows in excess of 10 bacteria per millilitre. Risk factors for the development of bacterial overgrowth include dysmotility; anatomical disturbances in the bowel, including fistulae, diverticula and blind loops created after surgery, and resection of the ileo-cecal valve; gastroenteritis-induced alterations to the small intestine; and the use of certain medications, including proton pump inhibitors.

Small bowel bacterial overgrowth syndrome is treated with an elemental diet or antibiotics, which may be given in a cyclic fashion to prevent tolerance to the antibiotics, sometimes followed by prokinetic drugs to prevent recurrence if dysmotility is a suspected cause.

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).

Tropical sprue is a malabsorption disease commonly found in tropical regions, marked with abnormal flattening of the villi and inflammation of the lining of the small intestine.

It differs significantly from coeliac sprue. It appears to be a more severe form of environmental enteropathy.

Lymphocytic colitis is a subtype of microscopic colitis, a condition characterized by chronic non-bloody watery diarrhea. The colonoscopy is normal but histology of the mucosal biopsy reveals an accumulation of lymphocytes in the colonic epithelium and connective tissue (lamina propria). Collagenous colitis shares this feature but additionally shows a distinctive thickening of the subepithelial collagen table. The peak incidence of lymphocytic colitis is in persons over age 50; the disease affects women and men equally. Lymphocytic colitis was first described in 1989.

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.

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.

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.

No definite cause has been determined. Some reports have implicated long-term usage of NSAIDs, proton pump inhibitors, and selective serotonin reuptake inhibitors, and other drugs. Associations with other autoimmune disorders suggests that overactive immune responses occur.

Microvillus inclusion disease, also known as Davidson's disease, congenital microvillus atrophy and, less specifically, microvillus atrophy (note: microvillus is often misspelled as microvillous), is a rare genetic disorder of the small intestine that is inherited in an autosomal recessive pattern.

It is characterized by chronic, intractable diarrhea in new-born infants, starting in the first few days of life.

This results in metabolic acidosis and severe dehydration. Pregnancy and birth are usually normal.

In addition to dietary problems, other causes of VAD are known. Iron deficiency can affect vitamin A uptake; other causes include fibrosis, pancreatic insufficiency, inflammatory bowel disease, and small-bowel bypass surgery. Excess alcohol consumption can deplete vitamin A, and a stressed liver may be more susceptible to vitamin A toxicity. People who consume large amounts of alcohol should seek medical advice before taking vitamin A supplements. In general, people should also seek medical advice before taking vitamin A supplements if they have any condition associated with fat malabsorption such as pancreatitis, cystic fibrosis, tropical sprue, and biliary obstruction. Other causes of vitamin A deficiency are inadequate intake, fat malabsorption, or liver disorders. Deficiency impairs immunity and hematopoiesis and causes rashes and typical ocular effects (e.g., xerophthalmia, night blindness).

The common cause of blindness in developing countries is VAD. The WHO estimates 13.8 million children to have some degree of visual loss related to VAD. Night blindness and its worsened condition, xerophthalmia, are markers of VAD, as it can also lead to impaired immune function, cancer, and birth defects. Collections of keratin in the conjunctiva, known as Bitot's spots, are also seen. Imtiaz's sign is the earliest ocular sign of VAD. Conjunctival epithelial defects occur around lateral aspect of the limbus in the subclinical stage of VAD. These conjunctival epithelial defects are not visible on a biomicroscope, but they take up black stain and become readily visible after instillation of kajal (surma); this is called "Imtiaz's sign". Vitamin A deficiency is one of several hypovitaminoses implicated in follicular hyperkeratosis.

Intraepithelial lymphocytes (IEL) are lymphocytes found in the epithelial layer of mammalian mucosal linings, such as the gastrointestinal (GI) tract and reproductive tract. However, unlike other T cells, IELs do not need priming. Upon encountering antigens, they immediately release cytokines and cause killing of infected target cells. In the GI tract, they are components of gut-associated lymphoid tissue (GALT).