Each part of the digestive system is subject to a wide range of disorders many of which can be congenital. Mouth diseases can also be caused by pathogenic bacteria, viruses, fungi and as a side effect of some medications. Mouth diseases include tongue diseases and salivary gland diseases. A common gum disease in the mouth is gingivitis which is caused by bacteria in plaque. The most common viral infection of the mouth is gingivostomatitis caused by herpes simplex. A common fungal infection is candidiasis commonly known as thrush which affects the mucous membranes of the mouth.
There are a number of esophageal diseases such as the development of Schatzki rings that can restrict the passageway, causing difficulties in swallowing. They can also completely block the esophagus.
Stomach diseases are often chronic conditions and include gastroparesis, gastritis, and peptic ulcers.
A number of problems including malnutrition and anemia can arise from malabsorption, the abnormal absorption of nutrients in the GI tract. Malabsorption can have many causes ranging from infection, to enzyme deficiencies such as exocrine pancreatic insufficiency. It can also arise as a result of other gastrointestinal diseases such as coeliac disease. Coeliac disease is an autoimmune disorder of the small intestine. This can cause vitamin deficiencies due to the improper absorption of nutrients in the small intestine. The  small intestine can also be obstructed by a volvulus, a loop of intestine that becomes twisted enclosing its attached mesentery. This can cause mesenteric ischemia if severe enough.
A common disorder of the bowel is diverticulitis. Diverticula are small pouches that can form inside the bowel wall, which can become inflamed to give diverticulitis. This disease can have complications if an inflamed diverticulum bursts and infection sets in. Any infection can spread further to the lining of the abdomen (peritoneum) and cause potentially fatal peritonitis.
Crohn's disease is a common chronic inflammatory bowel disease (IBD), which can affect any part of the GI tract, but it mostly starts in the terminal ileum.
Ulcerative colitis an ulcerative form of colitis, is the other major inflammatory bowel disease which is restricted to the colon and rectum. Both of these IBDs can give an increased risk of the development of colorectal cancer. Ulcerative colitis is the most common of the IBDs
Irritable bowel syndrome (IBS) is the most common of the functional gastrointestinal disorders. These are idiopathic disorders that the Rome process has helped to define.
Giardiasis is a disease of the small intestine caused by a protist parasite Giardia lamblia. This does not spread but remains confined to the lumen of the small intestine. It can often be asymptomatic, but as often can be indicated by a variety of symptoms. Giardiasis is the most common pathogenic parasitic infection in humans.
There are diagnostic tools mostly involving the ingestion of barium sulphate to investigate disorders of the GI tract. These are known as upper gastrointestinal series that enable imaging of the pharynx, larynx, oesophagus, stomach and small intestine and lower gastrointestinal series for imaging of the colon.