The most common sites for cancer of the GI tract are the colon and rectum. Together these colorectal cancers rank among the most frequent causes of cancer deaths in the United States in both men and women. A diet low in fiber and calcium and high in fat is a major risk factor in colorectal cancer. Heredity is also a factor, as is chronic inflammation of the colon (colitis). Polyps (growths) in the intestine often become cancerous and should be removed. Polyps can be identified and even removed by endoscopy.

One sign of colorectal cancer is bleeding into the intestine, which can be detected by testing the stool for blood. Because this blood may be present in very small amounts, it is described as occult ("hidden") blood. Colorectal cancers are staged according to Dukes classification, ranging from A to C according to severity.

The interior of the intestine can be observed with various endoscopes named for the specific area in which they are used, such as proctoscope (rectum), sigmoidoscope (sigmoid colon), colonoscope (colon).

In some cases of cancer, and for other reasons as well, it may be necessary to surgically remove a portion of the GI tract and create a stoma (opening) on the abdominal wall for elimination of waste. Such ostomy surgery is named for the organ involved, such as ileostomy (ileum) or colostomy (colon). When a connection (anastomosis) is formed between two organs of the tract, both organs are included in naming, such as gastroduodenostomy (stomach and duodenum) or coloproctostomy (colon and rectum).

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