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

A complete history and physical examination can be suggestive, especially if a palpable mass in the right lower quadrant of the abdomen is present (though this can be present in the absence of DIOS). Ultrasound and computed tomography (CT) imaging of the abdomen can confirm the diagnosis by demonstrating dilated loops of intestine with material in the intestinal lumen with bubbles. Air-fluid levels may be seen in those affected by DIOS.

Attempts must be made to determine whether there is a secondary cause amenable to treatment.

Primary (idiopathic) intestinal pseudo-obstruction is diagnosed based on motility studies, x-rays and gastric emptying studies.

There is no single, specific test for malabsorption. As for most medical conditions, investigation is guided by symptoms and signs. A range of different conditions can produce malabsorption and it is necessary to look for each of these specifically. Many tests have been advocated, and some, such as tests for pancreatic function are complex, vary between centers and have not been widely adopted. However, better tests have become available with greater ease of use, better sensitivity and specificity for the causative conditions. Tests are also needed to detect the systemic effects of deficiency of the malabsorbed nutrients (such as anaemia with vitamin B12 malabsorption).

Additional diagnoses which may present with similar symptoms to DIOS include severe constipation, appendicitis, and intussusception.

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.

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.

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.

HFM must be distinguished from cerebral folate deficiency (CFD)– a condition in which there is normal intestinal folate absorption, without systemic folate deficiency, but a decrease in CSF folate levels. This can accompany a variety of disorders. One form of CFD is due to loss-of-mutations in folate receptor-α, (FRα), which transports folates via an endocytic process. While PCFT is expressed primarily at the basolateral membrane of the choroid plexus, FRα, is expressed primarily at the apical brush-border membrane. Unlike subjects with HFM, patients with CFD present with neurological signs a few years after birth. The basis for the delay in the appearance of clinical manifestations due to loss of FRα function is not clear; the normal blood folate levels may be protective, although for a limited time.

Once a patient complains of dysphagia they should have an "upper endoscopy" (EGD). Commonly patients are found to have esophagitis and may have an esophageal stricture. Biopsies are usually done to look for evidence of esophagitis even if the EGD is normal. Usually no further testing is required if the diagnosis is established on EGD. Repeat endoscopy may be needed for follow up.

If there is a suspicion of a proximal lesion such as:

- history of surgery for laryngeal or esophageal cancer

- history of radiation or irritating injury

- achalasia

- Zenker's diverticulum

a "barium swallow" may be performed before endoscopy to help identify abnormalities that might increase the risk of perforation at the time of endoscopy.

If achalasia suspected an upper endoscopy is required to exclude a malignancy as a cause of the findings on barium swallow. Manometry is performed next to confirm. A normal endoscopy should be followed by manometry, and if manometry is also normal, the diagnosis is functional dysphagia.

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.

With early intervention, morbidity and mortality of cases of intestinal obstruction is low. The outcome is in part dependent upon congenital comorbidities and delays in diagnosis and management.

The CSF folate level is usually undetectable at the time of diagnosis. Even when the blood folate level is corrected, or far above normal, the CSF folate level remains low, consistent with impaired transport across the choroid plexus. The normal CSF folate level in children over the first three years of life is in the 75 to 150 nM range. In subjects with HFM it is very difficult indeed, rarely possible, to bring the CSF folate level into the normal range even with substantial doses of parenteral folate (see below).

It is important to note that both barium enema and colonoscopy are contraindicated during acute episodes of diverticulitis, as the barium may leak out into the abdominal cavity, and colonoscopy can cause perforations of the bowel wall.

Neonatal bowel obstruction is grouped into two general categories: high, or proximal, obstruction and low, or distal obstruction, both of which are suspected by failure to pass meconium at birth. High obstruction can be suspected based on the double bubble sign. Cases without distal gas are usually related to duodenal atresia, while high obstruction with distal gas need an upper gastrointestinal series because of the need to distinguish duodenal web, duodenal stenosis and annular pancreas from midgut volvulus, the latter being a surgical emergency. Confirmation is ultimately by surgical intervention.

A low obstruction is suspected on plain film, but needs follow up with a gastrografin enema, which itself can be therapeutic. The differential for low obstruction is ileal atresia, meconium ileus, meconium plug syndrome and Hirschsprung disease. In cases of meconium ileus or ileal atresia, the colon distal to the obstruction is hypoplastic, usually less than 1 cm in caliber, as development of normal colonic caliber "in utero" is due to the passage of meconium, which does not occur in either of these conditions. When diffusely small caliber is seen, it is referred to as microcolon. Radiographs in meconium ileus classically demonstrate a bubbly appearance in the right lower quadrant due to a combination of ingested air and meconium. If, on contrast enema, reflux into the dilated distal small bowel loops can be achieved, the study is both diagnostic and therapeutic, as the ionic contrast medium can dissolve the meconium to allow passage of enteric content into the unused colon.

If contrast cannot be refluxed into the distal small bowel, ileal atresia remains a diagnostic possibility. Jejunal and ileal atresia are caused by "in utero" vascular insults, leading to poor recanalization of distal small bowel segments, a condition in which surgical resection and reanastamosis are mandatory. Hirschsprung disease is due to an arrest in neural cell ganglia, leading to absent innervation of a segment distal bowel, and appears as a massively dilated segment of distal bowel on contrast enema. Surgical resection is necessary for this condition as well. Imperforate anus also requires surgical management, with the diagnosis made by inability to pass the rectal tube through the anal sphincter. Supportive intravenous hydration, gastric decompression, and ventilatory support may be needed due to poor neonatal nutrition resulting from dysfunctional bowel absorption.

In most regions, galactosemia is diagnosed as a result of newborn screening, most commonly by determining the concentration of galactose in a dried blood spot. Some regions will perform a second-tier test of GALT enzyme activity on samples with elevated galactose, while others perform both GALT and galactose measurements. While awaiting confirmatory testing for classic galactosemia, the infant is typically fed a soy-based formula, as human and cow milk contains galactose as a component of lactose. Confirmatory testing would include measurement of enzyme activity in red blood cells, determination of Gal-1-P levels in the blood, and mutation testing. The differential diagnosis for elevated galactose concentrations in blood on a newborn screening result can include other disorders of galactose metabolism, including galactokinase deficiency and galactose epimerase deficiency. Enzyme assays are commonly done using fluorometric detection or older radioactively labeled substrates.

Galactose is converted into glucose by the action of three enzymes, known as the Leloir pathway. There are diseases associated with deficiencies of each of these three enzymes:

Infants are routinely screened for galactosemia in the United States, and the diagnosis is made while the person is still an infant. Infants affected by galactosemia typically present with symptoms of lethargy, vomiting, diarrhea, failure to thrive, and jaundice. None of these symptoms are specific to galactosemia, often leading to diagnostic delays. Luckily, most infants are diagnosed on newborn screening. If the family of the baby has a history of galactosemia, doctors can test prior to birth by taking a sample of fluid from around the fetus (amniocentesis) or from the placenta (chorionic villus sampling or CVS).

A galactosemia test is a blood test (from the heel of the infant) or urine test that checks for three enzymes that are needed to change galactose sugar that is found in milk and milk products into glucose, a sugar that the human body uses for energy. A person with galactosemia doesn't have one of these enzymes. This causes high levels of galactose in the blood or urine.

Galactosemia is normally first detected through newborn screening, or NBS. Affected children can have serious, irreversible effects or even die within days from birth. It is important that newborns be screened for metabolic disorders without delay. Galactosemia can even be detected through NBS before any ingestion of galactose-containing formula or breast milk.

Detection of the disorder through newborn screening (NBS) does not depend on protein or lactose ingestion, and, therefore, it should be identified on the first specimen unless the infant has been transfused. A specimen should be taken prior to transfusion. The enzyme is prone to damage if analysis of the sample is delayed or exposed to high temperatures. The routine NBS is accurate for detection of galactosemia. Two screening tests are used to screen infants affected with galactosemia—the Beutler's test and the Hill test. The Beutler's test screens for galactosemia by detecting the level of enzyme of the infant. Therefore, the ingestion of formula or breast milk does not affect the outcome of this part of the NBS, and the NBS is accurate for detecting galactosemia prior to any ingestion of galactose.

Duarte galactosemia is a milder form of classical galactosemia and usually has no long term side effects.

Secondary chronic intestinal pseudo-obstruction is managed by treating the underlying condition.

There is no cure for primary chronic intestinal pseudo-obstruction. It is important that nutrition and hydration is maintained, and pain relief is given. Drugs that increase the propulsive force of the intestines have been tried, as have different types of surgery.

Proximal enteritis usually is managed medically. This includes nasogastric intubation every 1–2 hours to relieve gastric pressure secondary to reflux, which often produces to 2–10 L, as well as aggressive fluid support to maintain hydration and correct electrolyte imbalances. Maintaining hydration in these patients can be very challenging. In some cases, fluid support may actually increase reflux production, due to the decreased intravascular oncotic pressure from low total protein and albumin levels, leading to loss of much of these IV fluids into the intestinal lumen. These horses will often display dependent edema (edema that collects in locations based on gravity). Colloids such as plasma or Hetastarch may be needed to improve intravascular oncotic pressure, although they can be cost prohibitive for many owners. Reflux levels are monitored closely to help evaluate fluid losses, and horses recovering from DPJ show improved hydration with decreased reflux production and improved attitude.

Non-steroidal anti-inflammatory drugs (NSAIDs) are commonly used for pain relief, reduction of inflammation, and for their anti-endotoxin effects, but care must be taken since they may produce gastrointestinal ulceration and damage the kidneys. Due to a suspected link to "Clostridial" infection, anti-microbials are often administered, usually penicillin or metronidazole. Aminoglycosides should be used with extreme caution due to the risk of nephrotoxicosis (damage to the kidney). The mucosa of the intestines is damaged with DPJ, often resulting in absorption of endotoxin and risking laminitis, so therapy to combat and treat endotoxemia is often employed. This includes treatment with drugs that counteract endotoxin such as Polymyxin B and Bio-Sponge, fluid support, and laminitis prevention such as icing of the feet. Prokinetic drugs such as lidocaine, erythromycin, metoclopramide, and bethanechol are often used to treat the ileus associated with the disease.

Horses are withheld food until reflux returns to less than 1–2 L of production every 4 hours, and gut sounds return, often requiring 3–7 days of therapy. Parenteral nutrition is often provided to horses that are withheld feed for greater than 3–4 days. It is suspected to improve healing and shorten the duration of the illness, since horses often become cachexic due to the protein losing enteropathy associated with this disease.

Surgery may need to be performed to rule out colic with similar presenting signs such as obstruction or strangulation, and in cases that are long-standing (> 7 days) to perform a resection and anastomosis of the diseased bowel. However, some horses have recovered with long-term medical support (up to 20 days).

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.

The main diagnostic tools are blood tests, X-rays of the abdomen, CT scanning, and/or ultrasound. If a mass is identified, biopsy may determine the nature of the mass.

Radiological signs of bowel obstruction include bowel distension and the presence of multiple (more than six) gas-fluid levels on supine and erect abdominal radiographs.

Contrast enema or small bowel series or CT scan can be used to define the level of obstruction, whether the obstruction is partial or complete, and to help define the cause of the obstruction.

According to a meta-analysis of prospective studies by the Cochrane Collaboration, the appearance of water-soluble contrast in the cecum on an abdominal radiograph within 24 hours of oral administration predicts resolution of an adhesive small bowel obstruction with a pooled sensitivity of 97% and specificity of 96%.

Colonoscopy, small bowel investigation with ingested camera or push endoscopy, and laparoscopy are other diagnostic options.

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.

Most individuals with SBCADD are identified through newborn screening, where they present with an elevation of a five carbon acylcarnitine species. Confirmatory testing includes plasma and urine analysis to identify the carnitine and glycine conjugates of 2-methylbutyryl-CoA.

With acutely ill patients, consider emergency surgery laparotomy if there is a high index of suspicion.

Plain radiography may demonstrate signs of duodenal obstruction with dilatation of the proximal duodenum and stomach but it is often non-specific. Upper gastrointestinal series is the modality of choice for the evaluation of malrotation as it will show an abnormal position of the duodeno-jejunal flexure (ligament of Treitz). In cases of malrotation complicated with volvulus, it demonstrates a corkscrew appearance of the distal duodenum and jejunum. In cases of obstructing Ladd bands, it will reveal a duodenal obstruction.

In equivocal cases, contrast enema, may be helpful by showing the caecum at an abnormal location.

It is usually discovered near birth, but in some cases is not discovered until adulthood. In adults, the "whirlpool sign" of the superior mesenteric artery can be useful in identifying malrotation.