The disease is regarded as extremely rare, with an incidence (new number of cases per year) of one case per million people. The patients are predominantly male (86% in a survey of American patients), although in some countries the rate of women receiving a diagnosis of Whipple's disease has increased in recent years. It occurs predominantly in those of Caucasian ethnicity, suggesting a genetic predisposition in that population.

"T. whipplei" appears to be an environmental organism that is commonly present in the gasterointestinal tract but remains asymptomatic. Several lines of evidence suggest that some defect—inherited or acquired—in immunity is required for it to become pathogenic. The possible immunological defect may be specific for "T. whipplei", since the disease is not associated with a substantially increased risk of other infections.

The disease is usually diagnosed in middle age (median 49 years). Studies from Germany have shown that age at diagnosis has been rising since the 1960s.

Treatment is with penicillin, ampicillin, tetracycline, or co-trimoxazole for one to two years. Any treatment lasting less than a year has an approximate relapse rate of 40%. Recent expert opinion is that Whipple's disease should be treated with doxycycline with hydroxychloroquine for 12 to 18 months. Sulfonamides (sulfadiazine or sulfamethoxazole) may be added for treatment of neurological symptoms.

As a result of microbial symbiosis and immunity, alterations in enteral bacteria may contribute to inflammatory gut diseases. IBD-affected individuals have been found to have 30–50 percent reduced biodiversity of commensal bacteria, such as decreases in Firmicutes (namely Lachnospiraceae) and Bacteroidetes. Further evidence of the role of gut flora in the cause of inflammatory bowel disease is that IBD-affected individuals are more likely to have been prescribed antibiotics in the 2–5 year period before their diagnosis than unaffected individuals. The enteral bacteria can be altered by environmental factors, such as concentrated milk fats (a common ingredient of processed foods and confectionery) or oral medications such as antibiotics and oral iron preparations.

The epidemiology of Idiopathic sclerosing mesenteritis disease is extremely rare and has only been diagnosed in about an estimated 300 patients worldwide to date (as of 2014), it is probably under diagnosed.

It can occur in children.

IBD is a complex disease which arises as a result of the interaction of environmental and genetic factors leading to immunological responses and inflammation in the intestine.

Several causes of sclerosing mesenteritis have been suggested, but the principal pathophysiological mechanism is probably autoimmune. Trauma and prior surgical procedures have also been indicated as possibilities. It can be found in IgG4-related disease.

Environmental enteropathy is believed to result in chronic malnutrition and subsequent growth stunting (low height-for-age measurement) as well as other child development deficits.

In the 1960s, researchers reported a syndrome of non-specific histopathological and functional changes to the small intestine in individuals living in unsanitary conditions. This syndrome was observed predominantly in tropical regions across Latin America, sub-Saharan Africa and Asia. The geographic distribution of the syndrome lead to the original term of "tropical enteropathy" (sometimes also "tropical jejunopathy").

Following initial reports, further investigation revealed that these symptoms were not specific to tropical climates. For example, individuals in more wealthy tropical countries, such as Qatar and Singapore, did not exhibit these symptoms. Similarly, subsequent studies have shown this condition to be common across the developing world, closely associated with impoverished conditions but independent of climate or geography. As a result, the term "environmental enteropathy" was introduced to specify that this condition is not only found in tropical areas and is believed to be caused by environmental factors.

An increasing number of people are now surviving cancer, with improved treatments producing cure of the malignancy (cancer survivors). There are now over 14 million such people in the US, and this figure is expected to increase to 18 million by 2022. More than half are survivors of abdominal or pelvic cancers, with about 300,000 people receiving abdominal and pelvic radiation each year. It has been estimated there are 1.6 million people in the US with post-radiation intestinal dysfunction, a greater number than those with inflammatory bowel disease such as Crohn's disease or ulcerative colitis.

The following are causes of BHL:

- Sarcoidosis

- Infection

- Tuberculosis

- Fungal infection

- Mycoplasma

- Intestinal Lipodystrophy (Whipple's disease)

- Malignancy

- Lymphoma

- Carcinoma

- Mediastinal tumors

- Inorganic dust disease

- Silicosis

- Berylliosis

- Extrinsic allergic alveolitis

- Such as bird fancier's lung

- Less common causes also exist:

- Eosinophilic granulomatosis with polyangiitis

- Human immunodeficiency virus

- Extrinsic allergic alveolitis

- Adult-onset Still's disease

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.

A large number of people receive abdominal and or pelvic radiotherapy as part of their cancer treatment with 60–80% experiencing gastrointestinal symptoms. This is used in standard therapeutic regimens for cervical cancer, prostate cancer, rectal cancer, anal cancer, lymphoma and other abdominal malignancies. Symptoms can be made worse by the effects of surgery, chemotherapy or other drugs given to treat the cancer. Improved methods of radiotherapy have reduced the exposure of non-involved tissues to radiation, concentrating the effects on the cancer. However, as the parts of the intestine such as the ileum and the rectum are immediately adjacent to the cancers, it is impossible to avoid some radiation effects. Previous intestinal surgery, obesity, diabetes, tobacco smoking and vascular disorders increase the chances of developing enteropathy.

Human intestinal spirochetosis is caused by "Brachyspira pilosicoli" and "Brachyspira aalborgi". Porcine and avian intestinal spirochetosis are caused by "Brachyspira pilosicoli".

No clear association exists with complaints. However, potential associations exist with include watery diarrhea and abdominal pain, which may be seen with blood; these findings are not specific, i.e. may be seen due to number of other causes.

Pneumatosis intestinalis (also called intestinal pneumatosis, pneumatosis cystoides intestinalis, or pneumatosis coli) is of an intestine, that is, gas cysts in the bowel wall. As a radiological sign it is highly suggestive for necrotizing enterocolitis. This is in contrast to gas in the intestinal lumen (which is relieved by flatulence). In newborns, pneumatosis intestinalis is considered diagnostic for necrotizing enterocolitis, and the air is produced by bacteria in the bowel wall. The pathogenesis of pneumatosis intestinalis is poorly understood and is likely multifactorial. PI itself is not a disease, but rather a clinical sign. In some cases, PI is an incidental finding, whereas in others, it portends a life-threatening intra-abdominal condition.

Estimating the mortality rate based on the available literature is difficult. Several case reports have revealed an association between acquired partial lipodystrophy and other diseases.

Nephropathy, in the form of membranoproliferative glomerulonephritis, occurs in about 20% of patients. Usually, patients do not have clinically evident renal disease or abnormalities in renal function until they have had the disease for 8 or more years. Membranoproliferative glomerulonephritis usually presents with asymptomatic proteinuria or hematuria.

The disease may gradually progress. About 40-50% of patients develop end-stage renal disease over the course of 10 years. This condition is responsible for most recurrent hospital admissions in patients with acquired partial lipodystrophy. Rapid progression of renal disease in a pregnant patient was reported. Recurrent disease in transplanted kidneys is common, although there have been reports of successful transplantations.

Associated autoimmune diseases (e.g., systemic lupus erythematosus, thyroiditis) contribute significantly to increased morbidity in these patients compared with the general population. Although uncommon, insulin resistance increases cardiovascular risk. Susceptibility to bacterial infections probably results from a C3 deficiency (due to complement activation and consumption of C3). Low C3 levels may impair complement-mediated phagocytosis and bacterial killing.

Horses may develop pharyngitis, laryngitis, or esophagitis secondary to indwelling nasogastric tube. Other complications include thrombophlebitis, laminitis (which subsequently reduces survival rate), and weight loss. Horses are also at increased risk of hepatic injury.

Survival rates for DPJ are 25–94%. Horses that survive the incident rarely have reoccurrence.

Short bowel syndrome in adults and children is usually caused by surgery. This surgery may be done for:

- Crohn's disease, an inflammatory disorder of the digestive tract

- Volvulus, a spontaneous twisting of the small intestine that cuts off the blood supply and leads to tissue death

- Tumors of the small intestine

- Injury or trauma to the small intestine

- Necrotizing enterocolitis (premature newborn)

- Bypass surgery to treat obesity

- Surgery to remove diseases or damaged portion of the small intestine

Some children are also born with an abnormally short small intestine, known as congenital short bowel.

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.

Bilateral hilar lymphadenopathy is a bilateral enlargement of the lymph nodes of pulmonary hila. It is a radiographic term that describes the enlargement of mediastinal lymph nodes and is most commonly identified by a chest x-ray.

In primary chronic intestinal pseudo-obstruction (the majority of chronic cases), the condition may be caused by an injury to the smooth muscle (myopathic) or the nervous system (neuropathic) of the gastrointestinal tract.

In some cases there appears to be a genetic association. One form has been associated with DXYS154.

Secondary chronic intestinal pseudo-obstruction can occur as a consequence of a number of other conditions, including Kawasaki disease, Parkinson's disease, Chagas' disease, Hirschsprung's disease, intestinal hypoganglionosis, collagen vascular diseases, mitochondrial disease, endocrine disorders and use of certain medications. The term may be used synonymously with enteric neuropathy if a neurological cause is suspected.

Intestinal Connective tissue abnormality may cause Intestinal Desmosis The absence of the tendinous plexus layer was first described in 1998 by Meier-Ruge. Desmosis is implicated in disturbed gut motility.

Normal peristalsis depends upon the interaction between muscles, nerve cells and tendinous connective tissue. A malfunction of any of these leads to intestinal motility disorders.

Desmosis may be congenital (aplastic form) or acquired (atrophic form).

The "aplastic" form is rare. Typical clinical findings are hypoperistalsis, and pseudo-obstruction. These are found in premature infants, associated with low birth weight. The "atrophic" form is more frequent. Inflammation of the muscularis propria releases enzymes including collagenases which destroy the connective tissue of the bowel wall. Primarily newborns and small children are affected, although this manifestation can also be found in adults. The most common location is the colon with a necrotizing enterocolitis as well as Crohn Disease and diverticulitis. If the taenia are also affected, the disease is defined as complete atrophic desmosis, all other forms without involvement of the taenia are referred to as incomplete. Clinically, patients demonstrate chronic constipation.

As proposed by Giuseppe Martucciello, microscopic diagnosis requires laparoscopic intestinal full-thickness biopsies from colon. Histological findings are absence of the tendinous plexus layer and connective tissue fibers in longitudinal and circular muscle layer.

Around 250 cases have been reported since the recognition of this syndrome. It is a rare syndrome with no known prevalence, although it is more common than the generalized form of acquired lipodystrophy (Lawrence syndrome).

- Race: No clear relationship exists between incidence and race in this syndrome; however, most reported patients have been of European descent.

- Age: The median age of onset of lipodystrophy has been reported to be around seven years; however, onset occurring as late as the fourth or fifth decade of life also has been reported. The median age at presentation has been about 25 years, and women have been found to present later than men (age 28 for women, age 18 for men).

- Sex: Analysis of the pooled data revealed female patients were affected about four times more often than males.

Microvillus inclusion disease is thought to be extremely rare; only approximately 200 cases have been identified in children in Europe.

One patient, a teenage female living in Arizona, suddenly began to grow microvilli after thirteen years of TPN (Total Parenteral Nutrition) and Lipid dependency. She now enjoys a typical teenage diet and is seen regularly by her Gastroenterologist.

One patient from the UK was documented to achieve nutritional independence at age 3.

On 26 June 2009 a six-year-old girl diagnosed with microvillus inclusion disease became the third person in the UK to die of swine flu.

Surgical treatment remains the treatment of choice for cats and dogs diagnosed with intestinal tumors who are in otherwise good health.