Cyclospora cayetanensis is a coccidian protozoan. It appears that all human cases are caused by this species; no animal reservoirs for C. cayetanensis have been identified.
When freshly passed in stools, the oocyst is not infective (thus, direct fecal-oral transmission cannot occur; this differentiates Cyclospora from another important coccidian parasite, Cryptosporidium). In the environment , sporulation occurs after days or weeks at temperatures between 22°C to 32°C, resulting in division of the sporont into two sporocysts, each containing two elongate sporozoites . The sporulated oocysts can contaminate fresh produce and water which are then ingested . The oocysts excyst in the gastrointestinal tract, freeing the sporozoites, which invade the epithelial cells of the small intestine . Inside the cells they undergo asexual multiplication into type I and type II meronts. Merozoites from type I meronts likely remain in the asexual cycle, while merozoites from type II meronts undergo sexual development into macrogametocytes and microgametocytes upon invasion of another host cell. Fertilization occurs, and the zygote develops to an oocyst which is released from the host cell and shed in the stool . Several aspects of intracellular replication and development are still unknown, and the potential mechanisms of contamination of food and water are still under investigation.