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.

Definitive diagnosis is made by suction biopsy of the distally narrowed segment. A histologic examination of the tissue would show a lack of ganglionic nerve cells. Diagnostic techniques involve anorectal manometry, barium enema, and rectal biopsy.

The suction rectal biopsy is considered the current international gold standard in the diagnosis of Hirschsprung's disease.

Radiologic findings may also assist with diagnosis. Cineanography (fluoroscopy of contrast medium passing anorectal region) assists in determining the level of the affected intestines.

Alagille syndrome can be determined by a special kind of newborn screening wherein DNA samples are analyzed for markers in the JAG1 section. The DNA sequence patterns of a child will be analyzed for probabilistic deletions and therefore takes weeks to complete. After detection, the child should be treated with vitamins and necessary diet to develop the liver function postnatally.

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.

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.

Patients with abnormal cardiac and kidney function may be more at risk for hemolytic uremic syndrome

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.

Early treatment includes removing fluids from the stomach via a nasogastric tube, and providing fluids intravenously. The definitive treatment for duodenal atresia is surgery (duodenoduodenostomy), which may be performed openly or laparoscopically. The surgery is not urgent. The initial repair has a 5 percent morbidity and mortality rate.

Treatment of Hirschsprung's disease consists of surgical removal (resection) of the abnormal section of the colon, followed by reanastomosis.

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.

CCD may be detectable on prenatal ultrasound. After birth, signs in affected babies typically are abdominal distension, visible peristalsis, and watery stools persistent from birth that show chloride loss of more than 90 mmol/l.

An important feature in this diarrhea that helps in the diagnosis, is that it is the only type of diarrhea that causes metabolic alkalosis rather than metabolic acidosis.

The differential diagnosis of chronic and intractable diarrhea is:

- Intestinal epithelial dysplasia

- Syndromatic diarrhea

- Immunoinflammatory enteropathy

It is nearly always fatal unless, like short bowel syndrome patients, treated with parenteral nutrition or an intestinal transplant. The patient is often classified as being in "intestinal failure" and treated with the cohort of patients known as "short bowel syndrome" patients.

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).

The incidence of VACTERL association is estimated to be approximately 1 in 10,000 to 1 in 40,000 live-born infants. It is seen more frequently in infants born to diabetic mothers. While most cases are sporadic, there are clearly families who present with multiple involved members.

The diagnosis of duodenal atresia is usually confirmed by radiography. An X-ray of the abdomen shows two large air filled spaces, the so-called "double bubble" sign. The air is trapped in the stomach and proximal duodenum, which are separated by the pyloric sphincter, creating the appearance of two bubbles visible on x-ray. Since the closure of the duodenum is complete in duodenal atresia, no air is seen in the distal duodenum.

Atresias occurring distal to the duodenum are usually caused by vascular accidents or ischemic insult, such as jejunoileal atresia.

Early treatment is possible once the disease is detected. Once the classical symptoms appear, the best way to eliminate the dangers of Alagille syndrome is a full liver transplant. Most of the short-term treatments available are aimed at improving the functioning of the heart and reducing the effects of impaired liver, kidney, and spleen function.

Treatment is possible and these are the steps taken:

Resuscitate the patient with fluids to stabilize them before surgically

- correcting the malrotation (counterclockwise rotation of the bowel),

- cutting the fibrous bands over the duodenum,

- widening the mesenteric pedicle by separation of the duodenum and cecum.

With this condition the appendix is often on the wrong side of the body and therefore removed as a precautionary measure during the surgical procedure.

One surgical technique is known as "Ladd's procedure", after Dr. William Ladd. Long term research on the Ladd procedure shows that even after the procedure, patients are susceptible to have complaints and might need further surgery.

Although its cause is poorly understood, situs ambiguous has been linked to family history of malformations and maternal cocaine use, suggesting both genetic and environmental factors play a role. Several genes in the TGF-beta pathway, which controls left-right patterning of viseral organs across the body axis, have been indicated in sporadic and familial cases of atrial isomerism.

There does not appear to be a screening method for prevention of heterotaxy syndrome. However, genetic testing in family members that display atrial isomerism or other cardiac malformations may help to discern risk for additional family members, especially in X-linked causes of heterotaxy syndrome.

A 2007 study followed 112 individuals for a mean of 12 years (mean age 25.3, range 12–71). No patient died during follow-up, but several required medical interventions. The mean final heights were 167 and 153 cm for men and women, respectively, which is approximately 2 standard deviations below normal.

For proper diagnosis of situs ambiguous, cardiac and non-cardiac features must be evaluated. Diagnostic criteria for atrial isomerism includes observation of symmetry of thoracic visceral organs upon echocardiogram, arrhythmia upon electrocardiogram, and chest x-ray for confirmation of the heart's location across the left-right axis. In addition, a series of gastrointestinal tests can be conducted for observation of intestinal malrotation, as well as a scan of the liver and spleen for biliary function.

Available treatments address the symptoms of CCD, not the underlying defect. Early diagnosis and aggressive salt replacement therapy result in normal growth and development, and generally good outcomes. Replacement of NaCl and KCl has been shown to be effective in children.

A potential treatment is butyrate.

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.

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.

Umbilical cord ulceration and intestinal atresia is a rare congenital disease that leads to intestinal atresia, umbilical cord ulceration and severe intrauterine haemorrhage. Only 15 cases have so far been reported, though newer studies are beginning to conclude that this disease has a higher incidence rate than has been previously reported. A particular study has given intestinal atresia and umbilical cord ulceration a clear link after 5 such cases were reported at the time of publication.