Intestinal parasites are parasites that populate the gastro-intestinal tract in humans and other animals. They can live throughout the body, but most prefer the intestinal wall. Means of exposure include: ingestion of undercooked meat, drinking infected water, and skin absorption. A parasite is an organism that feeds off another organism, called a host.

The major groups of parasites include protozoans (organisms having only one cell) and parasitic worms (helminths). Of these, protozoans, including cryptosporidium, microsporidia, and isospora, are most common in HIV-infected persons. Each of these parasites can infect the digestive tract, and sometimes two or more can cause infection at the same time.

Parasites can get into the intestine by going through the mouth from uncooked or unwashed food, contaminated water or hands, or by skin contact with larva infected soil, they can also be transferred by the sexual act of anilingus in some cases. When the organisms are swallowed, they move into the intestine, where they can reproduce and cause symptoms. Children are particularly susceptible if they are not thoroughly cleaned after coming into contact with infected soil that is present in environments that they may frequently visit such as sandboxes and school playgrounds. People in developing countries are also at particular risk due to drinking water from sources that may be contaminated with parasites that colonize the gastrointestinal tract.