The causal agent is a single-celled coccidian parasite. The species designation Cyclospora cayetanensis was given in 1994 to Peruvian isolates of human-associated Cyclospora. It appears that all human cases are caused by this species.
When freshly passed in stools, the oocyst is not infective (thus, direct fecal-oral transmission is unlikely; this differentiates Cyclospora from another important coccidian parasite, Cryptosporidium). In the environment , sporulation usually requires at least 1–2 weeks at temperatures from 22°C to 32°C, and results in division of the sporont into two sporocysts, each containing two elongated sporozoites . Fresh produce and water can serve as vehicles for transmission , and the sporulated oocysts are ingested (in contaminated food or water) . 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 and sexual development to mature into oocysts, which will be shed in stools .