The role of "Helicobacter pylori" in functional dyspepsia is controversial, and no clear causal relationship has been established. This is true for both the symptom profile and pathophysiology of functional dyspepsia. Although some epidemiologic studies have suggested an association between "H. pylori" infection and functional dyspepsia, others have not. The discrepancy may stem in part from differences in methodology and lack of adequate consideration of confounding factors such as past history of peptic ulcer disease and socioeconomic status. Controlled trials disagree about whether or not "H. pylori" eradication is beneficial in functional dyspepsia, with roughly half of the trials showing improvement and the other half no improvement. In a recent multicenter U.S. trial that randomized 240 patients to treatment or placebo, and followed patients for 12 months, 28% of treated patients versus 23% of those receiving placebo reported relief of symptoms at the 12-month follow-up. Similarly, recent European trials have not shown significant differences in symptoms after "H. pylori" eradication as compared with controls. Systematic reviews of eradication have been conducted, with varying results. A systematic review in the Annals of Internal Medicine suggested no statistically significant effect, with an odds ratio (OR) for treatment success versus control of 1.29 (95% CI, 0.89–1.89; P = 0.18). Still, no effect was seen after adjusting for heterogeneity and for cure of "H. pylori". In contrast, a Cochrane review found a small but statistically significant effect in curing symptoms ("H. pylori" cure vs placebo, 36% vs 30%, respectively).

Acute, self-limited "dyspepsia" may be caused by overeating, eating too quickly, eating high-fat foods, eating during stressful situations, or drinking too much alcohol or coffee. Many medications cause dyspepsia, including aspirin, nonsteroidal anti-inflammatory drugs (NSAIDs), antibiotics (metronidazole, macrolides), diabetes drugs (metformin, Alpha-glucosidase inhibitor, amylin analogs, GLP-1 receptor antagonists), antihypertensive medications (angiotensin converting enzyme [ACE] inhibitors, Angiotensin II receptor antagonist), cholesterol-lowering agents (niacin, fibrates), neuropsychiatric medications (cholinesterase inhibitors [donepezil, rivastigmine]), SSRIs (fluoxetine, sertraline), serotonin-norepinephrine-reuptake inhibitors (venlafaxine, duloxetine), Parkinson drugs (Dopamine agonist, monoamine oxidase [MAO]-B inhibitors), corticosteroids, estrogens, digoxin, iron, and opioids.

Perforated peptic ulcer is a surgical emergency and requires surgical repair of the perforation. Most bleeding ulcers require endoscopy urgently to stop bleeding with cautery, injection, or clipping.

A 2009 study which followed 189 patients found no excess mortality despite the increased risk of pancreatic cancer.

H2 antagonists or proton-pump inhibitors decrease the amount of acid in the stomach, helping with healing of ulcers.

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.

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.

treatment of HP resemble that of chronic pancreatitis of other causes. Treatment focuses on enzyme and nutritional supplementation, pain management, pancreatic diabetes, and local organ complications, such as pseudocysts, bile duct or duodenal obstruction.(PMC1774562)

Other medical treatments have been tried and include estrogen and progesterone therapy, Corticostreoids are effective, but are "limited by their side effects."

GAVE is treated commonly by means of an endoscope, including argon plasma coagulation and electrocautery. Since endoscopy with argon photocoagulation is "usually effective", surgery is "usually not required". Coagulation therapy is well-tolerated but "tends to induce oozing and bleeding." "Endoscopy with thermal ablation" is favored medical treatment because of its low side effects and low mortality, but is "rarely curative." Treatment of GAVE can be categorized into endoscopic, surgical and pharmacologic. Surgical treatment is definitive but it is rarely done nowadays with the variety of treatment options available. Some of the discussed modalities have been used in GAVE patients with another underlying disease rather than SSc; they are included as they may be tried in resistant SSc-GAVE patients. Symptomatic treatment includes iron supplementation and blood transfusion for cases with severe anemia, proton pump inhibitors may ameliorate the background chronic gastritis and minute erosions that commonly co-existed in biopsy reports.

More than half of people with Crohn's disease have tried complementary or alternative therapy. These include diets, probiotics, fish oil and other herbal and nutritional supplements.

- Acupuncture is used to treat inflammatory bowel disease in China, and is being used more frequently in Western society. At this time, evidence is insufficient to recommend the use of acupuncture.

- A 2006 survey in Germany, found that about half of people with IBD used some form of alternative medicine, with the most common being homeopathy and a study in France found that about 30% used alternative medicine. Homeopathic preparations are not effective for treating any condition, with large-scale studies finding them to be no more effective than a placebo.

- There are contradicting studies regarding the effect of medical cannabis on inflammatory bowel disease.

Certain foods and lifestyle are considered to promote gastroesophageal reflux, but most dietary interventions have little supporting evidence. Avoidance of specific foods and of eating before lying down should be recommended only to those in which they are associated with the symptoms. Foods that have been implicated include coffee, alcohol, chocolate, fatty foods, acidic foods, and spicy foods. Weight loss and elevating the head of the bed are generally useful. A wedge pillow that elevates the head may inhibit gastroesophageal reflux during sleep. Stopping smoking and not drinking alcohol do not appear to result in significant improvement in symptoms. Although moderate exercise may improve symptoms in people with GERD, vigorous exercise may worsen them.

Crohn's may result in anxiety or mood disorders, especially in young people who may have stunted growth or embarrassment from fecal incontinence. Counselling as well as antidepressant or anxiolytic medication may help some people manage.

As of 2017 there is a small amount of research looking at mindfulness-based therapies, hypnotherapy, and cognitive behavioural therapy.

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.

The treatments for GERD include lifestyle modifications, medications, and possibly surgery. Initial treatment is frequently with a proton-pump inhibitor such as omeprazole.

The cancerous mass tends to block food from getting to the small intestine. If food cannot get to the intestines, it will cause pain, acid reflux, and weight loss because the food cannot get to where it is supposed to be processed and absorbed by the body.

Patients with duodenal cancer may experience abdominal pain, weight loss, nausea, vomiting, and chronic GI bleeding.

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.

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.

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.

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.

Meckel's diverticulum occurs in about 2% of the population. Prevalence in males is 3–5 times higher than in females. Only 2% of cases are symptomatic, which usually presents among children at the age of 2.

Most cases of Meckel's diverticulum are diagnosed when complications manifest or incidentally in unrelated conditions such as laparotomy, laparoscopy or contrast study of the small intestine. Classic presentation in adults includes intestinal obstruction and inflammation of the diverticulum (diverticulitis). Painless rectal bleeding most commonly occurs in toddlers.

Inflammation in the ileal diverticulum has symptoms that mimic appendicitis, therefore its diagnosis is of clinical importance. Detailed knowledge of the pathophysiological properties is essential in dealing with the life-threatening complications of Meckel's diverticulum.

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.

Treatment is aimed at removing the irritant or infection. "Helicobacter pylori" infection is usually treated with antibiotics.

Neonatal bowel obstruction (NBO) or neonatal intestinal obstruction is the most common surgical emergency in the neonatal period. It may occur due to a variety of conditions and has an excellent outcome based on timely diagnosis and appropriate intervention.

The exact causes are not known. It is not associated with a particular gene, but there is some evidence of recurrence in families.