Fetal and neonatal intestinal atresia are treated using laparotomy after birth. If the area affected is small, the surgeon may be able to remove the damaged portion and join the intestine back together. In instances where the narrowing is longer, or the area is damaged and cannot be used for period of time, a temporary stoma may be placed.

An intussusception is often suspected based on history and physical exam, including observation of Dance's sign. A digital rectal examination is particularly helpful in children, as part of the intussusceptum may be felt by the finger. A definite diagnosis often requires confirmation by diagnostic imaging modalities. Ultrasound is the imaging modality of choice for diagnosis and exclusion of intussusception, due to its high accuracy and lack of radiation. The appearance of target sign (also called "doughnut sign" on a sonograph, usually around 3 cm in diameter, confirms the diagnosis. The image seen on transverse sonography or computed tomography is that of a doughnut shape, created by the hyperechoic central core of bowel and mesentery surrounded by the hypoechoic outer edematous bowel. In longitudinal imaging, intussusception resembles a sandwich.

An x-ray of the abdomen may be indicated to check for intestinal obstruction or free intraperitoneal gas. The latter finding implies that bowel perforation has already occurred. Some institutions use air enema for diagnosis, as the same procedure can be used for treatment.

In a cecal volvulus, the cecum may be returned to a normal position and sutured in place, a procedure known as cecopexy. If identified early, before presumed intestinal wall ischemia has resulted in tissue breakdown and necrosis, the cecal volvulus can be detorsed laparoscopically.

In children, insussusception at the ileocecal junction and accounts for 90 percent of all cases.

A physical examination may reveal a mass or distention of the abdomen.

Tests which may be useful for diagnosis include:

- Abdominal x-ray

- Abdominal CT scan

- Contrast enema study

Treatment for sigmoid volvulus may include sigmoidoscopy. If the mucosa of the sigmoid looks normal and pink, place a rectal tube for decompression, correct any fluid, electrolyte, cardiac, renal or pulmonary abnormalities and then take the person to the operating room for repair. If surgery is not performed, there is a high rate of recurrence.

For people with signs of sepsis or an abdominal catastrophe, immediate surgery and resection is advised.

Gastroscopy, or endoscopic evaluation of the stomach, is useful in chronic cases of colic suspected to be caused by gastric ulcers, gastric impactions, and gastric masses. A 3-meter scope is required to visualize the stomach of most horses, and the horse must be fasted prior to scoping.

Treatment of accessory pancreas depends on the location and extent of the injured tissue. Surgery may be an option, or some physicians order prophylactic antibiotics.

Radiographs (x-rays) are sometimes used to look for sand and enteroliths. Due to the size of the adult horse's abdomen, it requires a powerful machine that is not available to all practitioners. Additionally, the quality of these images is sometimes poor.

On x-rays, gas may be visible in the abdominal cavity. Gas is easily visualized on x-ray while the patient is in an upright position. The perforation can often be visualised using computed tomography. White blood cells are often elevated.

Conservative treatment involves the long term use of laxatives and enemas, and has limited success. Dietary changes in order to control the disease are ineffective and high fiber diets often worsen the symptoms in children. As a last resort, surgical treatment (internal sphincter myectomy or colon resection) is used. In extreme cases, the only effective cure is a complete transplant of the affected parts.

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.

Intestinal atresias are often discovered before birth: either during a routine sonogram which shows a dilated intestinal segment due to the blockage, or by the development of polyhydramnios (the buildup of too much amniotic fluid in the uterus). These abnormalities are indications that the fetus may have a bowel obstruction which a more detailed ultrasound study can confirm.

Some fetuses with bowel obstruction have abnormal chromosomes. An amniocentesis is recommended because it can determine not only the sex of the baby, but whether or not there is a problem with the chromosomes.

Pancreatic disorders are often accompanied by weakness and fatigue. The past Medical history may reveal previous disorders of the biliary tract or duodenum, abdominal trauma or surgery, and metabolic disorders such as diabetes mellitus. The medication history should be detailed and specifically include the use of thiazides, furosemide, estrogens, corticosteroids, sulfonamides, and opiates. Note a family history of pancreatic disorders. In the review of systems, obtain a complete description of any pain in the upper abdomen or epigastric area. Symptoms that may be important in relation to pancreatic disorders are pruritus, abdominal pain, dyspnea, nausea, and vomiting. The functional assessment includes data about the patient’s dietary habits and use of alcohol.

Note any restlessness, flushing, or diaphoresis during the examination. Vital signs may disclose low-grade fever, tachypnea, tachycardia, and hypotension. Inspect the skin for jaundice. Assess the abdomen for distention, tenderness, discoloration, and diminished bowel sounds.

Tests and procedures used to diagnose pancreatic disorders include laboratory analyses of blood, urine, stool, and pancreatic fluid, and imaging studies. Specific blood studies used to assess pancreatic function include measurements of serum amylase, lipase, glucose, calcium, and triglyceride levels. Urine amylase and renal amylase clearance tests may also be ordered. Stool specimens may be analyzed for fat content. The secretin stimulation test measures the bicarbonate concentration of pancreatic fluid after secretin is given intravenously to stimulate the production of pancreatic fluid.

Although it would seem to be the better way to go in terms of management, there has been recent criticism on the need for such testing because of reliability issues. However, it must be stated that there are options such as the glucose breath test and jejunal aspiration the explanations of which are beyond the scope of this current article.

Duplications are usually removed surgically, even if they are found incidentally (i.e. not causing symptoms or encountered on routine studies for other reasons), as there is a high incidence of complications resulting from untreated cases. Cysts are often technically easier to remove than tubular malformations since tubular structures usually share a blood supply with the associated gut.

It can be grouped into NID A and NID B, with the "A" form affecting the sympathetic innervation, and the "B" version affecting the parasympathetic innervation.

In 2002 Martucciello G et al. published the first analysis of associated anomalies in IND population is an important clinical approach to investigate possible pathogenetic correlations. Two recessive syndromes were identified (3 families). The first was characterized by NID B, intestinal malrotation, and congenital short bowel, the second by NID B, short stature, mental retardation, and facial dysmorphism. In this study, gastrointestinal anomalies accounted for 67.4% of all associated disorders. These data suggest a strong correlation between IND and intestinal development.

Enteric duplication cysts, sometimes simply called duplication cysts, are rare congenital malformations of the gastrointestinal tract. They most frequently occur in the small intestine, particularly the ileum, but can occur anywhere along the gastrointestinal tract. They may be cystic or tubular in conformation.

The condition of having duplication cysts has been called intestinal duplication.

Symptoms of short bowel syndrome are usually addressed with medication. These include:

- Anti-diarrheal medicine (e.g. loperamide, codeine)

- Vitamin, mineral supplements and L-glutamine powder mixed with water

- H2 blocker and proton pump inhibitors to reduce stomach acid

- Lactase supplement (to improve the bloating and diarrhoea associated with lactose intolerance)

In 2004, the USFDA approved a therapy that reduces the frequency and volume of total parenteral nutrition (TPN), comprising: NutreStore (oral solution of glutamine) and Zorbtive (growth hormone, of recombinant DNA origin, for injection) together with a specialized oral diet. In 2012, an advisory panel to the USFDA voted unanimously to approve for treatment of SBS the agent teduglutide, a glucagon-like peptide-2 analog developed by NPS Pharmaceuticals, who intend to market the agent in the United States under the brandname Gattex. Teduglutide had been previously approved for use in Europe and is marketed under the brand Revestive by Nycomed.

Surgical procedures to lengthen dilated bowel include the Bianchi procedure, where the bowel is cut in half and one end is sewn to the other, and a newer procedure called serial transverse enteroplasty (STEP), where the bowel is cut and stapled in a zigzag pattern. Heung Bae Kim, MD, and Tom Jaksic, MD, both of Children's Hospital Boston, devised the STEP procedure in the early 2000s. The procedure lengthens the bowel of children with SBS and may allow children to avoid the need for intestinal transplantation. As of June 2009, Kim and Jaksic have performed 18 STEP procedures. The Bianchi and STEP procedures are usually performed by pediatric surgeons at quaternary hospitals who specialize in small bowel surgery.

Diagnosis of Pancreatic pseudocyst can be based on cyst fluid analysis:

- Carcinoembryonic antigen (CEA) and CEA-125 (low in pseudocysts and elevated in tumors);

- Fluid viscosity (low in pseudocysts and elevated in tumors);

- Amylase (usually high in pseudocysts and low in tumors)

The most useful imaging tools are:

- Ultrasonography – the role of ultrasonography in imaging the pancreas is limited by patient habitus, operator experience and the fact that the pancreas lies behind the stomach (and so a gas-filled stomach will obscure the pancreas).

- Computerized tomography – this is the gold standard for initial assessment and follow-up.

- Magnetic resonance cholangiopancreatography (MRCP) – to establish the relationship of the pseudocyst to the pancreatic ducts, though not routinely used

It is important to differentiate DPI from small intestinal obstruction, since obstruction may require surgical intervention, but this can at times be difficult. Horses suffering from DPI usually have a higher protein concentration in their peritoneal fluid compared to horses with small intestinal obstruction, often without a concurrent increase in nucleated cell count. They usually have some relief and decrease in pain after gastric decompression, while horses with an obstruction often still act colicky after nasogastric intubation. Distention of the small intestine may be less than what is felt on rectal examination of horses with obstruction, especially after gastric decompression. Horses with DPJ usually produce larger volumes of reflux (usually greater than 48 liters in the first 24 hours) than those with obstruction, and are often pyretic (temperatures of 101.5–102.5) and have alterations in white blood cell levels, while those with obstructions usually have a normal or lower than normal temperature and normal leukocyte levels.

Ultrasound can also be helpful to distinguish DPJ from obstruction. Horses with small intestinal obstruction will usually have an intestinal diameter of −10 cm with a wall thickness of 3–5mm. Horses with proximal enteritis usually have an intestinal diameter that is narrower, but wall thickness is often greater than 6mm, containing a hyperechoic or anechoic fluid, with normal, increased, or decreased peristalsis. However, obstructions that have been present for some time may present with thickened walls and distention of the intestine.

DPJ can only be definitively diagnosed during surgery or at necropsy, when its gross appearance of the small intestine may be evaluated.

Surgical intervention is nearly always required in form of exploratory laparotomy and closure of perforation with peritoneal wash. Occasionally they may be managed laparoscopically.

Conservative treatment including intravenous fluids, antibiotics, nasogastric aspiration and bowel rest is indicated only if the person is nontoxic and clinically stable.

Resection is sometimes a part of a treatment plan, but duodenal cancer is difficult to remove surgically because of the area that it resides in—there are many blood vessels supplying the lower body. Chemotherapy is sometimes used to try to shrink the cancerous mass. Other times intestinal bypass surgery is tried to reroute the stomach to intestine connection around the blockage.

A 'Whipple' procedure is a type of surgery that is sometimes possible with this cancer. In this procedure, the duodenum, a portion of the Pancreas (the head), and the gall bladder are usually removed, the small intestine is brought up to the Pylorus (the valve at the bottom of the stomach) and the Liver and Pancreas digestive enzymes and bile are connected to the small intestine below the Pylorus.

The removal of part of the Pancreas often requires taking Pancreatic Enzyme supplements to aid digestion. These are available in the form of capsules by prescription.

It is not unusual for a patient having received a Whipple procedure to feel perfectly well, and to lead his/her normal life without difficulty.

It is important for the procedure to be performed by a surgeon with extensive experience having done and observed the procedure, as specific competence makes a big difference.

Some patients need to be fitted with tubes to either add nutrients (feeding tubes) or drainage tubes to remove excess processed food that can not pass the blockage.

A Richter's hernia occurs when the antimesenteric wall of the intestine protrudes through a defect in the abdominal wall. This is discrete from other types of abdominal hernias in that only one intestinal wall protrudes through the defect, such that the lumen of the intestine is incompletely contained in the defect, while the rest remains in the peritoneal cavity. If such a herniation becomes necrotic and is subsequently reduced during hernia repair, perforation and peritonitis may result. A Richter's hernia can result in strangulation and necrosis in the absence of intestinal obstruction. It is a relatively rare but dangerous type of hernia.

Richter's hernia have also been noted in laparoscopic port-sites, usually when the fascia is not closed for ports larger than 10mm. A high index of suspicion is required in the post operative period as this sinister problem can closely mimic more benign complications like port-site haematomas.

Treatment is resection and anastomosis.

Mortality increases with delay in surgical intervention.

Diagnosis may be simple in cases where the patient's signs and symptoms are idiopathic to a specific cause. However this is generally not the case, considering that many pathogens which cause enteritis may exhibit the similar symptoms, especially early in the disease. In particular, "campylobacter, shigella, salmonella" and many other bacteria induce acute self-limited colitis, an inflammation of the lining of the colon which appears similar under the microscope.

A medical history, physical examination and tests such as blood counts, stool cultures, CT scans, MRIs, PCRs, colonoscopies and upper endoscopies may be used in order to perform a differential diagnosis. A biopsy may be required to obtain a sample for histopathology.