Cryptosporidium species are protozoan parasites that infect the epithelial cells of the gastrointestinal tract. In humans, infections occur primarily in the small intestine resulting in diarrheal illness. Cryptosporidium has a worldwide distribution and is considered an emerging zoonosis. Despite intensive efforts to develop workable experimental models, and the evaluation of nearly 1,000 chemotherapeutic agents, adequate therapies to clear the host of these parasites are still lacking. The reasons for the lack of drug efficacy are probably manifold and may include the unusual location of the parasite in the host cell, distinct structural and biochemical composition of drug targets, or its ability to either block import or rapidly efflux drug molecules. Understanding the basic mechanisms by which drugs are transported to the parasite and identifying unique targets are important steps in developing effective therapeutic agents.