If small and asymptomatic, no treatment is necessary. Larger, symptomatic cases of Zenker's diverticulum have been traditionally treated by neck surgery to resect the diverticulum and incise the cricopharyngeus muscle. However, in recent times non-surgical endoscopic techniques have gained more importance (as they allow for much faster recovery), and the currently preferred treatment is endoscopic stapling (i.e. diverticulotomy with staples ). This may be performed through a diverticuloscope. Other methods include fibreoptic diverticular repair.

Other non-surgical treatment modalities also exist, such as endoscopic laser, which recent evidence suggests is less effective than stapling.

Many people with diverticulosis have minimal to no symptoms, and do not require any specific treatment. Colonic stimulants should be avoided. Treatments, like some colon cleansers, that cause hard stools, constipation, and straining, are not recommended.

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.

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.

A high-fiber diet and fiber supplements are advisable to prevent constipation. The American Dietetic Association recommends 20–35 grams each day. Wheat bran has been shown to reduce intra colonic pressure.

The US National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) says foods such as nuts, popcorn hulls, sunflower seeds, pumpkin seeds, caraway seeds, and sesame seeds have traditionally been labeled as problem foods for people with this condition; however, no scientific data exists to prove this hypothesis. The seeds in tomatoes, zucchini, cucumbers, strawberries, raspberries, and poppy seeds, are not considered harmful by the NIDDK.

One study found that nuts and popcorn do not contribute positively or negatively to patients with diverticulosis or diverticular complications.

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

Medication (to prevent spasms) or Sphincterotomy (surgical procedure to cut the muscle) are the standard treatments for sphincter of Oddi dysfunction. One or the other may be better based on the classification of the condition.

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.

Pharmacological management may include anti-diarrheal/constipating agents and laxatives/stool bulking agents Stopping or substituting any previous medication that causes diarrhea may be helpful in some (see table). There is not good evidence for the use of any medications however.

In people who have undergone gallbladder removal, the bile acid sequestrant cholestyramine may help minor degrees of FI. Bulking agents also absorb water, so may be helpful for those with diarrhea. A common side effect is bloating and flatulence. Topical agents to treat and prevent dermatitis may also be used, such as topical antifungals when there is evidence of perianal candidiasis or occasionally mild topical anti-inflammatory medication. Prevention of secondary lesions is carried out by perineal cleansing, moisturization, and use of a skin protectant.

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.

Dietary modification may be important for successful management. Both diarrhea and constipation can contribute to different cases, so dietary advice must be tailored to address the underlying cause or it may be ineffective or counter productive. In persons with disease aggravated by diarrhea or those with rectal loading by soft stools, the following suggestions may be beneficial: increase dietary fiber; reduce wholegrain cereals/bread; reduce fruit and vegetables which contain natural laxative compounds (rhubarb, figs, prunes/plums); limit beans, pulses, cabbage and sprouts; reduce spices (especially chilli); reduce artificial sweeteners (e.g. sugar free chewing gum); reduce alcohol (especially stout, beer and ale); reduce lactose if there is some degree of lactase deficiency; and reduce caffeine. Caffeine lowers the resting tone of the anal canal and also causes diarrhea. Excessive doses of vitamin C, magnesium, phosphorus and/or calcium supplements may increase FI. Reducing olestra fat substitute, which can cause diarrhea, may also help.

In simple cases of obstruction, where there are no complications, a variety of non-surgical and surgical techniques are used to remove the enterolith. These include crushing the enterolith and milking it back to the stomach or forward to the colon, surgical removal via an uninvolved segment of the gastrointestinal tract, and resection of the involved segment.

The primary treatment for urethral diverticulum is surgical. The surgery is conducted transvaginally, usually when there is no acute inflammation to better aid dissection of the delicate tissues.

Surgery is recommended for some types of hernias to prevent complications like obstruction of the bowel or strangulation of the tissue, although umbilical hernias and hiatus hernias may be watched, or are treated with medication. Most abdominal hernias can be surgically repaired, but surgery has complications. Time needed for recovery after treatment is reduced if hernias are operated on laparoscopically. However, open surgery can be done sometimes without general anesthesia. Uncomplicated hernias are principally repaired by pushing back, or "reducing", the herniated tissue, and then mending the weakness in muscle tissue (an operation called herniorrhaphy). If complications have occurred, the surgeon will check the viability of the herniated organ and remove part of it if necessary.

Muscle reinforcement techniques often involve synthetic materials (a mesh prosthesis). The mesh is placed either over the defect (anterior repair) or under the defect (posterior repair). At times staples are used to keep the mesh in place. These mesh repair methods are often called "tension free" repairs because, unlike some suture methods (e.g., Shouldice), muscle is not pulled together under tension. However, this widely used terminology is misleading, as there are many tension-free suture methods that do not use mesh (e.g., Desarda, Guarnieri, Lipton-Estrin, etc.).

Evidence suggests that tension-free methods (with or without mesh) often have lower percentage of recurrences and the fastest recovery period compared to tension suture methods. However, among other possible complications, prosthetic mesh usage seems to have a higher incidence of chronic pain and, sometimes, infection.

The frequency of surgical correction ranges from 10 per 100,000 (U.K.) to 28 per 100,000 (U.S.).

Surgical correction of inguinal hernias is called a hernia repair. It is not recommended in minimally symptomatic hernias, for which watchful waiting is advised, due to the risk of post herniorraphy pain syndrome. Surgery is commonly performed as outpatient surgery. There are various surgical strategies which may be considered in the planning of inguinal hernia repair. These include the consideration of mesh use (e.g. synthetic or biologic), open repair, use of laparoscopy, type of anesthesia (general or local), appropriateness of bilateral repair, etc. Laparoscopy is most commonly used for non-emergency cases, however, a minimally invasive open repair may have a lower incidence of post-operative nausea and mesh associated pain. During surgery conducted under local anaesthesia, the patient will be asked to cough and strain during the procedure to help in demonstrating that the repair is without tension and sound.

Constipation after hernia repair results in strain to evacuate the bowel causing pain, and fear that the sutures may rupture. Opioid analgesia makes constipation worse. Promoting an easy bowel motion is important post-operatively.

Surgical correction is always recommended for inguinal hernias in child.

Emergency surgery for incarceration and strangulation carry much higher risk than planned, "elective" procedures. However, the risk of incarceration is low, evaluated at 0.2% per year. On the other hand, surgery has a risk of inguinodynia (10-12%), and this is why males with minimal symptoms are advised to watchful waiting. However, if they experience discomfort while doing physical activities or they routinely avoid them by the fear of pain, they should seek surgical evaluation. For female patients, surgery is recommended even for asymptomatic patients.

Left untreated, urethral diverticulum can cause significant morbidity (sickness).

During surgery, there is a risk for complications due to the highly vascular nature of the tissue. The urethral sphincters and its smooth muscle, as well as the neck of the bladder, can be injured regardless of the surgical approach. Other complications from surgery can include urinary incontinence, stress incontinence, a urethrovaginal fistula, or recurrent diverticula. Horseshoe-shaped diverticula and diverticula that completely surround the urethra are both associated with worse outcomes, as are those located close to the bladder, and large (over 3–4 cm) diverticula.

Treatment is surgical, potentially with a laparoscopic resection. In patients with bleeding, strangulation of bowel, bowel perforation or bowel obstruction, treatment involves surgical resection of both the Meckel's diverticulum itself along with the adjacent bowel segment, and this procedure is called a "small bowel resection". In patients without any of the aforementioned complications, treatment involves surgical resection of the Meckel's diverticulum only, and this procedure is called a simple diverticulectomy.

With regards to asymptomatic Meckel's diverticulum, some recommend that a search for Meckel's diverticulum should be conducted in every case of appendectomy/laparotomy done for acute abdomen, and if found, Meckel's diverticulectomy or resection should be performed to avoid secondary complications arising from it.

Diagnostic measures can be used as interventions to help stop bleeding in some cases. Bleeding that occurs due to a neoplasm (cancer growth) can be treated using colonoscopy and clipping, surgical intervention, or other measures, depending on the form and stage of cancer. Similarly, gastric cancer is treated depending on the staging, although typically requires surgical and medical therapy.

The treatment for motility issues, namely constipation, is typically to improve the movement of waste though the GI tract. This is done by using stool softeners (which work by pulling water into the stool while in the colon), addition of fiber to the diet, and use of osmotic laxatives (which help fluid movement through the colon, improving overall motility). Improving a persons gut motility can reduce the straining during defection and decrease the risk of developing of anal fissures. Anal fissures are associated with pain and blood on the toilet paper, and require time for healing. Treatment includes topical nitrates or calcium channel blockers and surgical interventions for chronic or complex cases. Similar to anal fissures, internal hemorrhoids can cause blood on the tissue when wiping, and be felt at the opening of the anus. Treatment options for hemorrhoids can be dependent on whether an underlying cause exists. An anorectal varices related hemorrhoids caused by cirrhosis, however symptomatic treatment often involves removal.

Colitis can be divided into infectious and drug induced, as can the treatment for these conditions. With infectious colitis, treatment is pathogen dependent, and generally requires the use of antibiotics. With drug-induced colitis, treatment typically involves removal of the offending agent, as is the case in NSAID induced PUD, however, removing radiation from a cancer patient is not always practical within a treatment regimen, so medical treatment is the primary mode of treatment.

Structural compromise leading to blood in stool is caused by a variety of conditions, and therefore requires different treatment for each condition. Peptic ulcer disease alone can be divided into multiple causes, but is generally initially controlled primarily with a proton pump inhibitor, with the addition of an H blocker, or in serious cases, requiring surgical intervention. Diverticulitis and diverticulosis require antibiotic treatment, and may require surgical intervention.

Inflammatory bowel disease is also divided into separate conditions, namely ulcerative colitis and Crohn's disease, which have different medical treatment regimens, and may require surgical intervention in more serious conditions.

Treatment involves an operation called a choledocholithotomy, which is the removal of the gallstone from the bile duct using ERCP, although surgeons are now increasingly using laparoscopy with cholangiography. In this procedure, tiny incisions are made in the abdomen and then in the cystic duct that connects the gallbladder to the bile duct, and a thin tube is introduced to perform a cholangiography. If stones are identified, the surgeon inserts a tube with an inflatable balloon to widen the duct and the stones are usually removed using either a balloon or tiny basket.

If laparoscopy is unsuccessful, an open choledocholithotomy is performed. This procedure may be used in the case of large stones, when the duct anatomy is complex, during or after some gallbladder operations when stones are detected, or when ERCP or laparoscopic procedures are not available.

Typically, the gallbladder is then removed, an operation called cholecystectomy, to prevent a future occurrence of common bile duct obstruction or other complications.

The treatment of pentalogy of Cantrell is directed toward the specific symptoms that are apparent in each individual. Surgical intervention for cardiac, diaphragmatic and other associated defects is necessary. Affected infants will require complex medical care and may require surgical intervention. In most cases, pentalogy of Cantrell is fatal without surgical intervention. However, in some cases, the defects are so severe that the individual dies regardless of the medical or surgical interventions received.

The specific treatment strategy will vary from one infant to another based upon various factors, including the size and type of abdominal wall defect, the specific cardiac anomalies that are present, and the particular type of ectopia cordis. Surgical procedures that may be required shortly after birth include repair of an omphalocele. At this time, physicians may also attempt to repair certain other defects including defects of the sternum, diaphragm and the pericardium.

In severe cases, some physicians advocate for a staged repair of the defects associated with pentalogy of Cantrell. The initial operation immediately after birth provides separation of the peritoneal and pericardial cavities, coverage of the midline defect and repair of the omphalocele. After appropriate growth of the thoracic cavity and lungs, the second stage consists of the repair of cardiac defects and return of the heart to the chest. Eventually, usually by age 2 or 3, reconstruction of the lower sternum or epigastrium may be necessary.

Other treatment of pentalogy of Cantrell is symptomatic and supportive.

There is currently no medical recommendation about how to manage an inguinal hernia condition in adults, due to the fact that, until recently, elective surgery used to be recommended. The hernia truss is intended to contain a reducible inguinal hernia within the abdomen. It is not considered to provide a cure, and if the pads are hard and intrude into the hernia aperture they may cause scarring and enlargement of the aperture. In addition, most trusses with older designs are not able effectively to contain the hernia at all times, because their pads do not remain permanently in contact with the hernia. The more modern variety of truss is made with non-intrusive flat pads and comes with a guarantee to hold the hernia securely during all activities. Although there is as yet no proof that such devices can prevent an inguinal hernia from progressing, they have been described by users as providing greater confidence and comfort when carrying out physically demanding tasks. A truss also increases the probability of complications, which include strangulation of the hernia, atrophy of the spermatic cord, and atrophy of the fascial margins. This allows the defect to enlarge and makes subsequent repair more difficult. Their popularity is likely to increase, as many individuals with small, painless hernias are now delaying hernia surgery due to the risk of post-herniorrhaphy pain syndrome. The elasticised pants used by athletes also provide useful support for the smaller hernia.

The benefits of the use of an external device to maintain reduction of the hernia without repairing the underlying defect (such as hernia trusses, trunks, belts, etc.) are unclear.

The fluid accumulation can be drained by aspiration, but this may be only temporary. A more permanent alternative is a surgical procedure, generally, an outpatient ambulatory (same-day) procedure, called a hydrocelectomy. There are two surgical techniques available for hydrocelectomy.

- Hydrocelectomy with Excision of the Hydrocele Sac: Incision of the hydrocele sac after complete mobilization of the hydrocele. Partial resection of the hydrocele sac, leaving a margin of 1–2 cm. Care is taken not to injure testicular vessels, epididymis or ductus deferens. The edge of the hydrocele sac is oversewn for hemostasis (von Bergmann's technique) or the edges are sewn together behind the spermatic cord (Winkelmann's or Jaboulay's technique). Hydrocele surgery with excision of the hydrocele sac is useful for large or thick-walled hydroceles and multilocular hydroceles.

- Hydrocele Surgery with Plication of the Hydrocele Sac: The hydrocele is opened with a small skin incision without further preparation. The hydrocele sac is reduced (plicated) by suture Hydrocele surgery: Lord's technique. The plication technique is suitable for medium-sized and thin-walled hydroceles. The advantage of the plication technique is the minimized dissection with a reduced complication rate.

If the hydrocele is not surgically removed, it may continue to grow. The hydrocele fluid can be aspirated. This procedure can be done in a urologist's office or clinic and is less invasive but, recurrence rates are high. Sclerotherapy, the injection of a solution following aspiration of the hydrocele fluid may increase success rates. In many patients, the procedure of aspiration and sclerotherapy is repeated as the hydrocele recurs.

Choledochal cysts are treated by surgical excision of the cyst with the formation of a roux-en-Y anastomosis hepaticojujenostomy/ choledochojujenostomy to the biliary duct.

Future complications include cholangitis and a 2% risk of malignancy, which may develop in any part of the biliary tree. A recent article published in Journal of Surgery suggested that choledochal cysts could also be treated with single-incision laparoscopic hepaticojejunostomy with comparable results and less scarring. In cases of saccular type of cyst, excision and placement of T-shaped tube is done.

Currently, there is no accepted indication for fetal intervention in the management of prenatally suspected choledochal cysts.

Hypospadias repair can be done in full-term, healthy infants at any time from 3 months of age. Premature babies generally have surgery done at 6 months or older. Using these guidelines, most babies can undergo repair as same-day surgery, without need to stay in the hospital afterwards.

The results of surgery are probably not influenced by the age at which repair is done, but older children are more likely to recall the event. Teens and adults typically spend one night in the hospital after surgery.