Cyclospora coyetanensis which is a recently described pathogen, is associated with prolonged diarrheae and history of travelling to tropical regions and intake of suspicious food and water. Cryptosporidium porvum is another pathogen that causes severe diarrhea defined initially in especially AIDS patients since 1980's. Cases of cyclosporiasis are frequently missed, since it is difficult to detect the parasite in human fecal samples, despite an increasing amount of data regarding this parasite. To identify both of these coccidian protozoa, faeces should be examined by modified acid-fast stain. Co-incidence of C.coyetanensis and C.porvum is seen rarely in Turkey. In this case report, C.cayetanensis and C.parvum found in a 28 years old pregnant women living in continental climate and without a history of travel, were presented. The patient had prolonged diarrhea and investigation of the feces by modified acid-fast and carbol fuchsin stains revealed C.coyetonensis and C.porvum. The immunoglobulin and lymphocyte subgroup testing done for the evaluation of the immune status of the patient, were all within normal limits. Following treatment with trimethoprim-sulfamethoxazole for 15 days, the oocyst number in feces has decreased. However, hepatic vein thrombosis and liver failure have developed in the postnatal period and she was diagnosed as Budd-Chiari syndrome. It was concluded that when the effect of pregnancy on immunity was taken into account, C.coyetonensis and C.parvum should be considered in cases of prolonged diarrhoeae in pregnant women.