Parasites in the genus Blastocystis comprise several subtypes (genotypes) and have a worldwide distribution. In some surveys, these are the most common parasites found in human stool specimens. An emerging literature suggests that the pathogenicity of Blastocystis is related to specific subtypes and parasite burden, although even individuals with small numbers of cysts may be symptomatic. Some data suggest an association between infection with Blastocystis and irritable bowel syndrome. However, there are few clinical studies demonstrating a direct relationship between the presence of this parasite and disease, few animal models to explore this relationship, and no consensus as to appropriate treatment. We recommend that asymptomatic individuals with few cysts not be treated. However, those who have gastrointestinal or dermatologic signs and symptoms and many cysts in stool specimens may require treatment. Metronidazole is the drug of choice. Additional studies are required to determine pathogenicity and appropriate therapy.