Cyclospora cayetanensis is an intestinal protozoon that has emerged as an important cause of endemic or epidemic diarrheal disease in children and adults worldwide. Cases of cyclosporiasis have been frequently missed, since it is difficult to detect the parasite in fecal sample, despite an increasing amount of data regarding this parasite. In this case report two patients admitted to hospital with complaints of diarrhea and abdominal pain, were presented. Blood and urine biochemistry of both of the patients were within the normal limits and no pathogenic bacteria were grown in their stool samples. Occult blood in stool were negative in both cases. Both of the cases had normal serum immunoglobulin levels and had negative viral hepatitis, HIV and autoimmune markers. Direct microscopic examination and modified acid-fast staining of the stool samples revealed C.cayetanensis oocysts. Clinical response and eradication of the parasite were achieved with two weeks trimethoprim/sulphamethoxazole (2 x 160/240 mg) therapy. Since both cases applied in July 2009, an epidemiological investigation was initiated, however, no relation was determined. Although Cyclospora infections are assumed to be endemic in our country, the sporadic case reports might be attributed to the lack of relevant information about the parasite by the clinicians, lack of appropriate laboratory diagnosis and specialized personel for parasitic examination. Thus, screening studies performed with appropriate diagnostic methods for Cyclospora, might provide more informative epidemiological data related to this infection in Turkey.