We evaluated the incidence of Cyclospora cayetanensis in immunocompetent, diarrheic patients during the summers of 2006-2009 in Istanbul. Stools from 1876 patients were examined using microscopic techniques. Cyclospora oocysts were observed in wet preparations by light and epifluorescence microscopy and in fecal smears that were stained by Kinyoun's modified acid-fast stain. Characteristic Cyclospora oocysts were observed in 2 patients in 2006, 17 in 2007, and one in 2009. Samples positive for Cyclospora were further analyzed by a single step polymerase chain reaction (PCR) with Cyclospora-specific primers from the ITS-1 region of the genome.