Intestinal atresia is a malformation resulting in narrowing or absence of a portion of the intestine. Duodenal atresia is the most common type, followed by ileal atresia. Hirschsprung's disease is an issue of innervation in the large intestine that can result in narrowing due to contraction, but there is no structural malformation in the bowel itself. Malrotation and volvulus are often seen together when a part of the intestine does not anchor or turn correctly during formation (malrotation) and then becomes twisted around itself (volvulus), resulting in constriction and loss of function.

Intussusception occurs when part of the intestine folds into another section of intestine, much like a telescope. This results in sharp, crampy, or colicky abdominal pain, vomit of bile, and bloody red "currant jelly" stool. Black stool and "coffee ground" emesis are both symptoms of upper gastrointestinal bleeding (stomach, generally), while projectile vomiting may be associated with pyloric stenosis.

The most common location for diverticulitis is the sigmoid colon. This area generally has increased pressure as compared to the rest of the large intestine and is especially vulnerable to weakness in the muscle layers of the colon wall.

While Crohn's disease can affect any part of the alimentary canal, the small intestine, particularly the terminal ileum, is the most common site of serosal inflammation. 

The characteristic histological alteration seen in ulcerative colitis is the crypt abscess, in which inflammation causes loss of goblet cells due to neutrophilic exudate in glandular lumens. Granulomas, thickened mucosa, and skip lesions are all seen in Crohn's disease.

In congenital hypertrophic pyloric stenosis, the smooth muscle of the pylorus becomes thickened, decreasing the lumen size of the pylorus. This prevents food from passing out of the stomach and into the small intestine, resulting in vomiting which is often projectile and tends to be non-bilious. Intussusception may show vomiting, but the more obvious sign is bloody "currant jelly" stools. Infant gastroesophageal reflux disease (GERD) may result in frequent spitting up, but projectile vomiting is rare. Diverticulitis is generally a condition of the elderly and tends to present as abdominal pain with alterations in bowel function and mild fever. 

Esophageal varices are most commonly seen in patients with cirrhosis due to portal hypertension. Gastroesophageal reflux disease (GERD) is associated with esophagitis and occasionally with metaplastic changes. Neither hiatal hernia nor achalasia are associated with esophageal varices.

While an infant with Hirshsprung's disease may have vomiting and bloody stool, the most common sign is failure to pass meconium within 48 hours of delivery. Hirschsprung's disease, which is an absence of innervation to the large intestine, which results in narrowing and constriction of one part of the bowel and dilation of the preceding segment, can be diagnosed by biopsy of the distally narrowed segment of the bowel.

While individuals with Celiac disease can certainly have gastritis, fistulas, and ulceration due to inflammation, the primary effect of Celiac disease is villous atrophy in the small intestine. Villi become blunted, leading to loss of ability to absorb nutrients, including minerals and fat-soluble vitamins. 

Mallory–Weiss syndrome refers to bleeding from partial-thickness tears in the mucosa at the junction of the stomach and esophagus, often from trauma such as violent retching or coughing. This is compared to Boerhaave's syndrome, which is a full-thickness tear of the esophageal wall. Esophagitis is most commonly caused by gastroesophageal reflux disease (GERD) and does not present with bleeding. Barrett's esophagus refers to a type of metaplasia in the lower esophagus which is thought to be caused by chronic GERD.