Wet-tail is a disease in the animal's intestines caused by the bacteria, "Lawsonia intracellularis". Wet-tail is a stress related illness—such stress can be caused by a variety of factors, including:

- Too much handling

- Change in environment

- Change in diet

- Extremely unclean caging

- Being away from mother and/or siblings

- Illness or death of a pair-bond or mate

Wet-tail or proliferative ileitis, is a disease of hamsters. It is precipitated by stress. Even with treatment, the animal can die within 48–72 hours. Baby hamsters are much more likely to get the disease than older hamsters. It commonly is found when the hamster is being weaned at about four weeks of age.

The primary route of transmission has not yet been identified, but direct contact may result in its transmission to developing embryos in viviparous species and eggs in oviparous species. Venereal transmission is also indicated as a possibility. The snake mite, "Ophionyssus natricis", has been implicated as a possible vector for the virus, since mite infestations are commonly seen in epizootics of IBD and in captive specimens of these snakes. Mites are sometimes very difficult to eradicate due to their resistance to certain toxins used to eliminate them.

Permethrin is known to be effective against mite infestations, but should be used with great caution and only in small quantities due to their toxic nature. Also, several nonchemical substances may be just as effective. These biological agents are sprayed onto the infested animal and desiccate the mites, rendering them unable to lay their eggs or consume blood beneath the scales of their host. The incubation period for mite eggs is thought to be about 10–14 days, so the treatment should be repeated after 10 days to ensure that any eggs that hatch or larvae that develop into nymphs are also quickly eliminated from the host before reaching sexual maturity and able to repeat their reproduction cycle.

Currently, the most effective treatment is transferring the affected fish to a freshwater bath for a period of 2 to 3 hours. This is achieved by towing the sea cages into fresh water, or pumping the fish from the sea cage to a tarp filled with fresh water. Mortality rates have been lowered by adding Levamisole to the water until the saturation is above 10ppm. Due to the difficulty and expense of treatment, the productivity of salmon aquaculture is limited by access to a source of fresh water. Chloramine and chlorine dioxide have also been used. Other potential in-feed treatments such as immunosupportive-based feeds, mucolytic compounds such as L-cysteine ethyl ester and the parasticide bithionol have been tested with some success although not developed for commercial use.

Amoebic gill disease (AGD) is a potentially fatal disease of some marine fish. It is caused by "Neoparamoeba perurans", the most important amoeba in cultured fish. It primarily affects farm raised fish of the Salmonidae family, most notably affecting the Tasmanian Atlantic Salmon (Salmo salar) industry, costing the A$20 million a year in treatments and lost productivity. Turbot, bass, bream, sea urchins and crabs have also been infected.

The disease has also been reported affecting the commercial salmon fisheries of the United States, Australia, New Zealand, France, Spain, Ireland and Chile. It was first diagnosed in the summer of 1984/1985 in populations of Atlantic Salmon off the east coast of Tasmania and was found to be caused by the "Neoparamoeba perurans" n.sp.

To date, no treatment for IBD is known. Snakes diagnosed with or suspected of having IBD should be euthanized because progression and transmission of the virus is both very rapid and destructive. All newly acquired snakes should, therefore, be quarantined for at least 3 and preferably 6 months before being introduced into established collections. The recommended period of quarantine for any wild-caught boa or python is at least 4–6 months.

Digital dermatitis is a disease that causes lameness in cattle. It was first discovered in Italy in 1974 by Cheli and Mortellaro. This disease is caused by a mixture of different bacteria. Anaerobic bacteria, including spirochetes of the genus "Treponema", are found in the lesions associated with the infection. Digital dermatitis is different from foot rot in cattle and both conditions may occur concurrently.

Digital dermatitis primarily affects dairy cattle and has been known to lower the quantity of milk produced, but the quality of the milk is unaffected.

Evidence show that risk factors favouring digital dermatitis outbreaks include: poor hygiene and high humidity; introduction of infected animals; no hoof care for heifers and dry cows; high levels of chronically infected animals; insufficient or inadequate hoof trimming; soft hooves and unbalanced nutrition.

Some systemic diseases can become symptomatic as a skin disorder. These include many endocrine (hormonal) abnormalities, such as hypothyroidism, Cushing's Syndrome (hyperadrenalcorticism), and tumors of the ovaries or testicles.

Some diseases are inherent abnormalities of skin structure or function. These include seborrheic dermatitis, ichthyosis, skin fragility syndrome (Ehlers-Danlos), hereditary canine follicular dysplasia and hypotrichosis, such as color dilution alopecia.

Juvenile cellulitis, also known as puppy strangles, is a skin disease of puppies of unknown etiology, which most likely has a hereditary component related to the immune system.

Treatment of lesions of digital dermatitis is done by topical application of agents to the affected skin. The skin should be cleaned and kept dry prior treatment. Topical oxytetracycline (OTC) is often referred as the most reliable treatment as cows treated with OTC have a good recovery rate. Bandaging the lesion is often undertaken but there is no evidence of any benefit and bandaging can provide the anaerobic environment which supports the spirochaetes.. Systemic antibiotics are not needed.

Control and prevention of digital dermatitis relies on prompt detection, isolation and treatment of affected cattle. Group hoof disinfection can be achieved via the passage of the cows through footbaths of antimicrobial solutions. Slurry build-up should be avoided since organic matter can impair the antimicrobial efficacy of the footbath solutions. Regular footbaths should be organised, using formalin, copper sulphate or a thymol-based disinfectant. While regular footbathing can help prevent hoof infections, occasional flare-up of active M2 lesions can happen.

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.

Across all posited aetiologies, contact granulomas are more commonly observed in male patients than in female patients, and more commonly in adult patients than in pediatric patients. In cases where gastroesophageal reflux disease is identified as the most likely cause of the granuloma, the patient is most commonly an adult man in his 30s or 40s. When contact granulomas do occur in female and pediatric patients, they usually occur post-intubation. There are no observable age or gender trends within the category of post-intubation patients suffering from contact granulomas, nor within the causation category of vocal abuse history.

For patients in need of tracheal intubation to receive oral drugs, an oversized tube, excessive movement of the tube, or infection can lead to contact granulomas, but this is rare.

In Germany, 90% of cases of infectious enteritis are caused by four pathogens, Norovirus, Rotavirus, "Campylobacter" and "Salmonella". Other common causes of infectious enteritis include bacteria such as "Shigella" and "E. coli," as well as viruses such as adenovirus, astrovirus and calicivirus. Other less common pathogens include "Bacillus cereus, Clostridium perfringens, Clostridium difficile" and "Staphylococcus aureus".

"Campylobacter jejuni" is one of the most common sources of infectious enteritis, and the most common bacterial pathogen found in 2 year old and smaller children with diarrhoea. It has been linked to consumption of contaminated water and food, most commonly poultry and milk. The disease tends to be less severe in developing countries, due to the constant exposure which people have with the antigen in the environment, leading to early development of antibodies.

Rotavirus is responsible for infecting 140 million people and causing 1 million deaths each year, mostly in children younger than 5 years. This makes it the most common cause of severe childhood diarrhoea and diarrhea-related deaths in the world. It selectively targets mature enterocytes in the small intestine, causing malabsorption, as well as inducing secretion of water. It has also been observed to cause villus ischemia, and increase intestinal motility. The net result of these changes is induced diarrhoea.

Enteritis necroticans is an often fatal illness, caused by β-toxin of "Clostridium perfringens". This causes inflammation and segments of necrosis throughout the gastrointestinal tract. It is most common in developing countries, however has also been documented in post-World War II Germany. Risk factors for enteritis necroticans include decreased trypsin activity, which prevent intestinal degradation of the toxin, and reduced intestinal motility, which increases likelihood of toxin accumulation.

"Y. enterocolitica" infections are sometimes followed by chronic inflammatory diseases such as arthritis, erythema nodosum, and reactive arthritis. This is most likely because of some immune-mediated mechanism.

"Y. enterocolitica" seems to be associated with autoimmune Graves-Basedow thyroiditis.

Whilst indirect evidence exists, direct causative evidence is limited,

and "Y. enterocolitica" is probably not a major cause of this disease, but may contribute to the development of thyroid autoimmunity arising for other reasons in genetically susceptible individuals.

"Y. enterocolitica" infection has also been suggested to not be the cause of autoimmune thyroid disease, but rather is only an associated condition, with both having a shared inherited susceptibility.

More recently, the role for "Y. enterocolitica" has been disputed.

Rare diseases are usually genetic and are therefore chronic. EURORDIS estimates that at least 80% of them have identified genetic origins. Other rare diseases are the result of infections and allergies or due to degenerative and proliferative causes.

Symptoms of some rare diseases may appear at birth or in childhood, whereas others only appear once adulthood is reached.

Research publications emphasize rare diseases that are chronic or incurable, although many short-term medical conditions are also rare diseases.

Ischemic enteritis is uncommon compared to ischemic colitis due to the highly vascularised nature of the small intestine, allowing for sufficient blood flow in most situations. It develops due to circulatory shock of mesenteric vessels in the absence of major vessel occlusion, often associated with an underlying condition such as hypertension, arrhythmia or diabetes. Thus it has been considered to be associated with atherosclerosis. Surgical treatment is usually required due to the likelihood of stenosis or complete occlusion of the small intestine. Ischemic damage can range from mucosal infarction, which is limited only to the mucosa; mural infarction of the mucosa and underlying submucosa; to transmural infarction of the full thickness of the gastrointestinal wall. Mucosal and mural infarcts in and of themselves may not be fatal, however may progress further to a transmural infarct. This has the potential for perforation of the wall, leading to peritonitis.

Yersiniosis is usually self-limiting and does not require treatment. For severe infections (sepsis, focal infection) especially if associated with immunosuppression, the recommended regimen includes doxycycline in combination with an aminoglycoside. Other antibiotics active against "Y. enterocolitica" include trimethoprim-sulfamethoxasole, fluoroquinolones, ceftriaxone, and chloramphenicol. "Y. enterocolitica" is usually resistant to penicillin G, ampicillin, and cephalotin due to beta-lactamase production.

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.

Oesophageal diseases include a spectrum of disorders affecting the oesophagus. The most common condition of the oesophagus in Western countries is gastroesophageal reflux disease, which in chronic forms is thought to result in changes to the epithelium of the oesophagus, known as Barrett's oesophagus.

Acute disease might include infections such as oesophagitis, trauma caused ingestion of corrosive substances, or rupture of veins such as oesophageal varices, Boerhaave syndrome or Mallory-Weiss tears. Chronic diseases might include congenital diseases such as Zenker's diverticulum and esophageal webbing, and oesophageal motility disorders including the nutcracker oesophagus, achalasia, diffuse oesophageal spasm, and oesophageal stricture.

Oesophageal disease may result in a sore throat, throwing up blood, difficulty swallowing or vomiting. Chronic or congenital diseases might be investigated using barium swallows, endoscopy and biopsy, whereas acute diseases such as reflux may be investigated and diagnosed based on symptoms and a medical history alone.

In medicine, Aschoff bodies are nodules found in the hearts of individuals with rheumatic fever. They result from inflammation in the heart muscle and are characteristic of rheumatic heart disease. These nodules were discovered independently by Ludwig Aschoff and Paul Rudolf Geipel, and for this reason they are occasionally called Aschoff-Geipel bodies.

Carrión's disease, or Oroya fever, or Peruvian wart is a rare infectious disease found only in Peru, Ecuador, and Colombia. It is endemic in some areas of Peru, is caused by infection with the bacterium "Bartonella bacilliformis", and transmitted by sandflies of genus "Lutzomyia".

Cat scratch disease occurs worldwide. Cats are the main reservoir of "Bartonella henselae", and the bacterium is transmitted to cats by the cat flea "Ctenocephalides felis". Infection in cats is very common with a prevalence estimated between 40-60%, younger cats being more commonly infective. Cats usually become immune to the infection, while dogs may be very symptomatic. Humans may also acquire it through flea or tick bites from infected dogs, cats, coyotes, and foxes.

Trench fever, produced by "Bartonella quintana" infection, is transmitted by the human body louse "Pediculus humanus corporis". Humans are the only known reservoir. Thorough washing of clothing may help to interrupt the transmission of infection.

A possible role for ticks in transmission of "Bartonella" species remains to be elucidated; in November 2011, "Bartonella rochalimae", "B. quintana", and "B. elizabethae" DNA was first reported in "Rhipicephalus sanguineus" and "Dermacentor nitens" ticks in Peru.

Enteropathy refers to any pathology of the intestine. Although enteritis specifically refers to an inflammation of the intestine, and is thus a more specific term than "enteropathy", the two phrases are sometimes used interchangeably.

Denture-related stomatitis is common and occurs worldwide. Usually the people affected are middle aged or elderly, with females being affected slightly more commonly than males. Prevalences of up to 70% have been reported in elderly care home residents. It is by far the most common type of oral candidiasis.

The increased incidence of Crohn's in the industrialized world indicates an environmental component. Crohn's is associated with an increased intake of animal protein, milk protein and an increased ratio of omega-6 to omega-3 polyunsaturated fatty acids.

Those who consume vegetable proteins appear to have a lower incidence of Crohn's disease. Consumption of fish protein has no association.

Smoking increases the risk of the return of active disease (flares). The introduction of hormonal contraception in the United States in the 1960s is associated with a dramatic increase in incidence, and one hypothesis is that these drugs work on the digestive system in ways similar to smoking. Isotretinoin is associated with Crohn's. Although stress is sometimes claimed to exacerbate Crohn's disease, there is no concrete evidence to support such claim. Dietary microparticles, such as those found in toothpaste, have been studied as they produce effects on immunity, but they were not consumed in greater amounts in patients with Crohn's.