The causes are divided into benign or malignant.

- Benign

- Peptic ulcer disease

- Infections, such as tuberculosis; and infiltrative diseases, such as amyloidosis.

- A rare cause of gastric outlet obstruction is blockage with a gallstone, also termed "Bouveret's syndrome".

- In children congenital pyloric stenosis / congenital hypertrophic pyloric stenosis may be a cause.

- A pancreatic pseudocyst can cause gastric compression.

- Pyloric mucosal diaphragm could be a rare cause.

- Malignant

- Tumours of the stomach, including adenocarcinoma (and its linitis plastica variant), lymphoma, and gastrointestinal stromal tumours

In a peptic ulcer it is believed to be a result of edema and scarring of the ulcer, followed by healing and fibrosis, which leads to obstruction of the gastroduodenal junction (usually an ulcer in the first part of the duodenum).

Immediate treatment is the most important factor in a favorable prognosis. A delay in treatment greater than six hours or the presence of peritonitis, sepsis, hypotension, or disseminated intravascular coagulation are negative prognostic indicators.

Historically, GDV has held a guarded prognosis. Although "early studies showed mortality rates between 33% and 68% for dogs with GDV," studies from 2007 to 2012 "reported mortality rates between 10% and 26.8%". Mortality rates approach 10% to 40% even with treatment. A study determined that with prompt treatment and good preoperative stabilization of the patient, mortality is significantly lessened to 10% overall (in a referral setting). Negative prognostic indicators following surgical intervention include postoperative cardiac arrhythmia, splenectomy, or splenectomy with partial gastric resection. Interestingly, a longer time from presentation to surgery was associated with a lower mortality, presumably because these dogs had received more complete preoperative fluid resuscitation and were thus better cardiovascularly stabilized prior to the procedure.

As a general rule, GDV is of greatest risk to deep-chested dogs. The five breeds at greatest risk are Great Danes, Weimaraners, St. Bernards, Gordon Setters, and Irish Setters. In fact, the lifetime risk for a Great Dane to develop GDV has been estimated to be close to 37 percent. Standard Poodles are also at risk for this health problem, as are Irish Wolfhound, Doberman Pinschers, Rottweilers, German Shorthaired Pointer, German Shepherds, Rhodesian Ridgebacks. Basset Hounds and Dachshunds have the greatest risk for dogs less than .

Meckel's diverticulum occurs in about 2% of the population. Prevalence in males is 3–5 times higher than in females. Only 2% of cases are symptomatic, which usually presents among children at the age of 2.

Most cases of Meckel's diverticulum are diagnosed when complications manifest or incidentally in unrelated conditions such as laparotomy, laparoscopy or contrast study of the small intestine. Classic presentation in adults includes intestinal obstruction and inflammation of the diverticulum (diverticulitis). Painless rectal bleeding most commonly occurs in toddlers.

Inflammation in the ileal diverticulum has symptoms that mimic appendicitis, therefore its diagnosis is of clinical importance. Detailed knowledge of the pathophysiological properties is essential in dealing with the life-threatening complications of Meckel's diverticulum.

The lifetime risk for a person with Meckel's diverticulum to develop certain complications is about 4–6%. Gastrointestinal bleeding, peritonitis or intestinal obstruction may occur in 15–30% of symptomatic patients (Table 1). Only 6.4% of all complications requires surgical treatment; and untreated Meckel's diverticulum has a mortality rate of 2.5–15%.

Table 1 – Complications of Meckel's Diverticulum:

Gastric volvulus of unknown cause comprises two thirds of cases and is presumably due to abnormal laxity of the gastrosplenic, gastroduodenal, gastrophrenic, and gastrohepatic ligaments. Type 1 gastric volvulus is more common in adults but has been reported in children.

Neonates with TEF or esophageal atresia are unable to feed properly. Once diagnosed, prompt surgery is required to allow the food intake. Some children do experience problems following TEF surgery; they can develop dysphagia and thoracic problems. Children with TEF can also be born with other abnormalities, most commonly those described in VACTERL association - a group of anomalies which often occur together, including heart, kidney and limb deformities. 6% of babies with TEF also have a laryngeal cleft.

Many causes exist including:

- diverticulitis : most common ~ 60%

- colorectal cancer (CRC) : ~ 20%

- Crohn's disease : ~ 10%

- radiotherapy

- appendicitis

- trauma

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.

If fecal matter passes through the fistula into the bladder, the existence of the fistula may be revealed by pneumaturia or fecaluria.

The combined type of gastric volvulus is a rare form in which the stomach twists mesentericoaxially and organoaxially. This type of gastric volvulus makes up the remainder of cases and is usually observed in patients with chronic volvulus.

Surgical repair can sometimes result in complications, including:

- Stricture, due to gastric acid erosion of the shortened esophagus

- Leak of contents at the point of anastomosis

- Recurrence of fistula

- Gastro-esophageal reflux disease

- Dysphagia

- Asthma-like symptoms, such as persistent coughing/wheezing

- Recurrent chest infections

- Tracheomalacia

Most damage to the pyloric valve occurs as a complication of gastric surgery. Other causes of biliary reflux may be:

- Peptic ulcer

- Gallbladder surgery (cholecystectomy)

A significant fraction of cases are idiopathic, with no identified specific etiology.

Biliary reflux, bile reflux or duodenogastric reflux is a condition that occurs when bile flows upward (refluxes) from the duodenum into the stomach and esophagus.

Biliary reflux can be confused with acid reflux, also known as gastroesophageal reflux disease (GERD). While bile reflux involves fluid from the small intestine flowing into the stomach and esophagus, acid reflux is backflow of stomach acid into the esophagus. These conditions are often related, and differentiating between the two can be difficult.

Bile is a digestive fluid made by the liver, stored in the gallbladder, and discharged into duodenum after food is ingested to aid in the digestion of fat. Normally, the pyloric sphincter prevents bile from entering the stomach. When the pyloric sphincter is damaged or fails to work correctly, bile can enter the stomach and then be transported into the esophagus as in gastric reflux. The presence of small amounts of bile in the stomach is relatively common and usually asymptomatic, but excessive refluxed bile causes irritation and inflammation.

Diagnosis is typically via a CT angiography, esophagogastroduodenoscopy, or arteriography. It is part of the differential diagnosis of gastrointestinal bleeding.

It can occur as a complication following biliary trauma (such as cholelithiasis), as an iatrogenic effect or as a result of a penetrating injury.

Dietary factors such as spice consumption, were hypothesized to cause ulcers until late in the 20th century, but have been shown to be of relatively minor importance. Caffeine and coffee, also commonly thought to cause or exacerbate ulcers, appear to have little effect. Similarly, while studies have found that alcohol consumption increases risk when associated with "H. pylori" infection, it does not seem to independently increase risk. Even when coupled with "H. pylori" infection, the increase is modest in comparison to the primary risk factor.

This list of diagnoses include diseases in which the wall of the bowel is compromised by disease.

- Peptic ulcer disease—divided into either duodenal or gastric ulcers, most common common causes include:

- Non steroidal anti-inflammatory drug (NSAID)—the use of these medications results in a structural change in the wall of the gut, namely ulcers, and potential blood in the stool.

- "H. pylori" infection—this bacterial infection can erode the wall of the stomach or duodenum, leading to a structural change in the stomach wall and bleeding in the stool.

- Chronic disease

- Diverticulitis and diverticulosis result from an out pouching of the colonic mucosa, or gut wall, leading to a break down of weak gut wall and an increased susceptibility to infection due to the bacteria in the GI tract, thus the potential for vascular compromise, the collection of bacteria in the area of perforation (abscess), the abnormal formation of communication between another part of the hollow GI tract (fistula), or blockage of the bowel (obstruction).

- Meckel's diverticulum is a congenital remnant of the omphalo-mesenteric duct that connected the fetal yolk sac to the intestines which is normal closed off and destroyed during the process of development. If a portion, or all of this duct remains a diverticulum or fistula can result, leading to the potential for a source of bleeding.

Diseases causing inflammation in the GI tract can lead to blood in the stool. Inflammation can occur anywhere along the GI tract in Crohn's disease, or in the colon if a person has ulcerative colitis.

- Crohns disease

- Ulcerative colitis

Stress due to serious health problems such as those requiring treatment in an intensive care unit is well described as a cause of peptic ulcers, which are termed stress ulcers.

While chronic life stress was once believed to be the main cause of ulcers, this is no longer the case. It is, however, still occasionally believed to play a role. This may be by increasing the risk in those with other causes such as "H. pylori" or NSAID use.

Rectovestibular fistula is the most common defect of the rectum and anal canal in females.

A biliary fistula often occurs in be suspected in a person who has recently undergone a surgical procedure, Pain may occur if the leaked bile is also infected, which can subsequently lead to biliary peritonitis.

Extensive ascites may accumulate, especially in the setting of sterile bile leakage, which is often asymptomatic in nature.

An aortoenteric fistula is a connection between the aorta and the intestines, stomach, or esophageus. There can be significant blood loss into the intestines resulting in bloody stool and death. It is usually secondary to an abdominal aortic aneurysm repair.

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.