The first stage of treatment used to be a reversible colostomy. In this approach, the healthy end of the large intestine is cut and attached to an opening created on the front of the abdomen. The contents of the bowel are discharged through the hole in the abdomen and into a bag. Later, when the patient's weight, age, and condition are right, the "new" functional end of the bowel is connected with the anus. The first surgical treatment involving surgical resection followed by reanastomosis without a colostomy occurred as early as 1933 by Doctor Baird in Birmingham on a one-year-old boy.

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

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.

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.

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.

The "treat empirically" route also has its difficulties, which have all come under wide debate and study. Recommendations are varied but seem to find some common ground around the notion that treatment should be individualized to the specific circumstances under which a patient has developed BLS since these circumstances affect the complex microbial make up of the affected bowel.

Tetracyclines have been the mainstay of treatment for BLS, but recent studies have concluded Rifaximin to be very effective in the treatment of BLS. One study by Di Stefano et al., however, concluded Metronidazole to be more effective than Rifaximin in the treatment of BLS.

Surgical management is reserved for fixing anatomical causes of bowel obstruction that interfere with normal function once they are amenable to such intervention. These conditions include:

- Strictures

- Fistulae

- Diverticula

These hernias should be repaired because of the high risk of strangulation; fortunately, surgery is straightforward, with only larger defects requiring a mesh prosthesis. Varied Spigelian hernia mesh repair techniques have been described, although evidence suggests laparoscopy results in less morbidity and shorter hospitalization compared with open procedures. Mesh-free laparoscopic suture repair is feasible and safe. This novel uncomplicated approach to small Spigelian hernias combines the benefits of laparoscopic localization, reduction, and closure without the morbidity and cost associated with foreign material.

If the anemia is severe, blood transfusion is required before any other intervention is considered. Endoscopic treatment is an initial possibility, where cautery or argon plasma coagulation (APC) treatment is applied through the endoscope. Failing this, angiography and emolization with particles is another microinvasive treatment option, which avoids the need for surgery and bowel resection. Here, the vessel supplying the angiodysplasia is selectively catheterized and embolizaed with microparticles. Resection of the affected part of the bowel may be needed if the other modalities fail. However, the lesions may be widespread, making such treatment impractical.

If the bleeding is from multiple or inaccessible sites, systemic therapy with medication may be necessary. First-line options include the antifibrinolytics tranexamic acid or aminocaproic acid. Estrogens can be used to stop bleeding from angiodysplasia. Estrogens cause mild hypercoaguability of the blood. Estrogen side effects can be dangerous and unpleasant in both sexes. Changes in voice and breast swelling is bothersome in men, but older women often report improvement of libido and perimenopausal symptoms. (The worries about hormone replacement therapy/HRT, however, apply here as well.)

In difficult cases, there have been positive reports about octreotide and thalidomide.

In severe cases or cases not responsive to either endoscopic or medical treatment, surgery may be necessary to arrest the bleeding.

In the management of small bowel obstructions, a commonly quoted surgical aphorism is: "never let the sun rise or set on small-bowel obstruction" because about 5.5% of small bowel obstructions are ultimately fatal if treatment is delayed. However improvements in radiological imaging of small bowel obstructions allow for confident distinction between simple obstructions, that can be treated conservatively, and obstructions that are surgical emergencies (volvulus, closed-loop obstructions, ischemic bowel, incarcerated hernias, etc.).

A small flexible tube (nasogastric tube) may be inserted through the nose into the stomach to help decompress the dilated bowel. This tube is uncomfortable but does relieve the abdominal cramps, distention, and vomiting. Intravenous therapy is utilized and the urine output is monitored with a catheter in the bladder.

Most people with SBO are initially managed conservatively because in many cases, the bowel will open up. Some adhesions loosen up and the obstruction resolves. However, when conservative management is undertaken, the patient is examined several times a day, and X-ray images are obtained to ensure that the individual is not getting clinically worse.

Conservative treatment involves insertion of a nasogastric tube, correction of dehydration and electrolyte abnormalities. Opioid pain relievers may be used for patients with severe pain. Antiemetics may be administered if the patient is vomiting. Adhesive obstructions often settle without surgery. If the obstruction is complete a surgery is usually required.

Most patients do improve with conservative care in 2–5 days. However, on some occasions, the cause of obstruction may be a cancer and in such cases, surgery is the only treatment. These individuals undergo surgery where the cause of SBO is removed. Individuals who have bowel resection or lysis of adhesions usually stay in the hospital a few more days until they are able to eat and walk.

Small bowel obstruction caused by Crohn's disease, peritoneal carcinomatosis, sclerosing peritonitis, radiation enteritis, and postpartum bowel obstruction are typically treated conservatively, i.e. without surgery.

Some causes of bowel obstruction may resolve spontaneously; many require operative treatment. In adults, frequently the surgical intervention and the treatment of the causative lesion are required. In malignant large bowel obstruction, endoscopically placed self-expanding metal stents may be used to temporarily relieve the obstruction as a bridge to surgery, or as palliation. Diagnosis of the type of bowel obstruction is normally conducted through initial plain radiograph of the abdomen, luminal contrast studies, computed tomography scan, or ultrasonography prior to determining the best type of treatment.

The condition is not usually immediately life-threatening. The intussusception can be treated with either a barium or water-soluble contrast enema or an air-contrast enema, which both confirms the diagnosis of intussusception, and in most cases successfully reduces it. The success rate is over 80%. However, approximately 5–10% of these recur within 24 hours.

Cases where it cannot be reduced by an enema or the intestine is damaged require surgical reduction. In a surgical reduction, the surgeon opens the abdomen and manually squeezes (rather than pulls) the part that has telescoped. If the surgeon cannot successfully reduce it, or the bowel is damaged, they resect the affected section. More often, the intussusception can be reduced by laparoscopy, pulling the segments of intestine apart with forceps.

Intussusception may become a medical emergency if not treated early, as it eventually causes death if not reduced. In developing countries where medical hospitals are not easily accessible, especially when other problems complicate the intussusception, death becomes almost inevitable. When intussusception or any other severe medical problem is suspected, the person must be taken to a hospital immediately.

The outlook for intussusception is excellent when treated quickly, but when untreated it can lead to death within two to five days. It requires fast treatment, because the longer the intestine segment is prolapsed the longer it goes without bloodflow, and the less effective a non-surgical reduction is. Prolonged intussusception also increases the likelihood of bowel ischemia and necrosis, requiring surgical resection.

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.

Most cases of simple, uncomplicated diverticulitis respond to conservative therapy with bowel rest.

If bacterial infection is suspected, antibiotics may be used. Despite being recommended by several guidelines, the use of antibiotics in mild cases of uncomplicated diverticulitis is supported with only "sparse and of low quality" evidence, with no evidence supporting their routine use.

Treatment consists primarily of supportive care including providing bowel rest by stopping enteral feeds, gastric decompression with intermittent suction, fluid repletion to correct electrolyte abnormalities and third-space losses, support for blood pressure, parenteral nutrition, and prompt antibiotic therapy. Monitoring is clinical, although serial supine and left lateral decubitus abdominal x-rays should be performed every six hours. Where the disease is not halted through medical treatment alone, or when the bowel perforates, immediate emergency surgery to resect the dead bowel is generally required, although abdominal drains may be placed in very unstable infants as a temporizing measure. Surgery may require a colostomy, which may be able to be reversed at a later time. Some children may suffer from short bowel syndrome if extensive portions of the bowel had to be removed.

No specific treatment or cure exists. Affected children usually need total parenteral nutrition through a central venous catheter. Further worsening of liver damage should however be avoided if possible. Diarrhea will likely continue even though food stops passing through the gastrointestinal system. They can subsequently be managed with tube feeding, and some may be weaned from nutritional support during adolescence.

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.

Proton pump inhibitors (such as omeprazole and lansoprazole) and histamine H2-receptor antagonists (such as famotidine and ranitidine) are used to slow acid secretion. Once gastric acid is suppressed, symptoms normally improve.

Resection of the polyps is required only if serious bleeding or intussusception occurs. Enterotomy is performed for removing large, single nodules. Short lengths of heavily involved intestinal segments can be resected. Colonoscopy can be used to snare the polyps if they are within reach.

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.

Once a child is born prematurely, thought must be given to decreasing the risk for developing NEC. Toward that aim, the methods of providing hyperalimentation and oral feeds are both important. In a 2012 policy statement, the American Academy of Pediatrics recommended feeding preterm infants human milk, finding "significant short- and long-term beneficial effects," including reducing the rate of NEC by a factor of two or more.

A study by researchers in Peoria, IL, published in "Pediatrics" in 2008, demonstrated that using a higher rate of lipid (fats and/or oils) infusion for very low birth weight infants in the first week of life resulted in zero infants developing NEC in the experimental group, compared with 14% with NEC in the control group. (They started the experimental group at 2 g/kg/d of 20% IVFE and increased within two days to 3 g/kg/d; amino acids were started at 3 g/kg/d and increased to 3.5.)

Neonatologists at the University of Iowa reported on the importance of providing small amounts of trophic oral feeds of human milk starting as soon as possible, while the infant is being primarily fed intravenously, in order to prime the immature gut to mature and become ready to receive greater oral intake. Human milk from a milk bank or donor can be used if mother's milk is unavailable. The gut mucosal cells do not get enough nourishment from arterial blood supply to stay healthy, especially in very premature infants, where the blood supply is limited due to immature development of the capillaries, so nutrients from the lumen of the gut are needed.

A Cochrane review published in April 2014 has established that supplementation of probiotics enterally "prevents severe NEC as well as all-cause mortality in preterm infants."

Increasing amounts of milk by 30 to 40 ml/kg is safe in infant who are born weighing very little. Not beginning feeding an infant by mouth for more than 4 days does not appear to have protective benefits.

Data from the NICHD Neonatal Research Network's Glutamine Trial showed that the incidence of NEC among extremely low birthweight (ELBW, <1000 g) infants fed with more than 98% human milk from their mothers was 1.3%, compared with 11.1% among infants fed only preterm formula, and 8.2% among infants fed a mixed diet, suggesting that infant deaths could be reduced by efforts to support production of milk by mothers of ELBW newborns.

Research from the University of California, San Diego found that higher levels of one specific human milk oligosaccharide, disialyllacto-N-tetraose, may be protective against the development of NEC.

Some surgeons choose to perform "key-hole" or laparoscopic surgery (also called minimally invasive surgery) rather than conventional "open" surgery. With minimally invasive surgery, one or more small incisions are made that allow the surgeon to use a surgical camera and small tools to repair the hernia.

Either open or minimally invasive surgery may be performed under general or regional anaesthesia, depending on the extent of the intervention needed. Three approaches have been described for open surgery.

- Lockwood’s infra-inguinal approach

- Lotheissen‘s trans-inguinal approach

- McEvedy’s high approach

The infra-inguinal approach is the preferred method for elective repair. The trans-inguinal approach involves dissecting through the inguinal canal and carries the risk of weakening the inguinal canal. McEvedy’s approach is preferred in the emergency setting when strangulation is suspected. This allows better access to and visualisation of bowel for possible resection. In any approach, care should be taken to avoid injury to the urinary bladder which is often a part of the medial part of the hernial sac.

Repair is either performed by suturing the inguinal ligament to the pectineal ligament using strong non-absorbable sutures or by placing a mesh plug in the femoral ring. With either technique care should be taken to avoid any pressure on the femoral vein.

Femoral hernias, like most other hernias, usually need operative intervention. This should ideally be done as an elective (non-emergency) procedure. However, because of the high incidence of complications, femoral hernias often need emergency surgery.