Cyclospora cayetanensis and Cryptosporidium spp are the two emerging coccidian parasites causing human infections by inhabiting the intestinal tract and can either remain asymptomatically, or can cause endemic and epidemic diarrhea in both children and adults. In the present study, the prevalence of C. cayetanensis and Cryptosporidium spp were assessed in an epidemiological study in Izmir province, along with risk factors related to infection. A total of 873 individuals from both the city centre and counties were included in the study, and stool samples were examined with formalin ethyl acetate and Kinyoun acid-fast stained preparations. The prevalence of C. cayetanensis and Cryptosporidium spp were found to be 3.0% and 0.8%, respectively. Lower socio-economic conditions, lack of health insurance, consumption of tap water, eating in common places were all found to be associated with higher positivity for C. cayetanensis and Cryptosporidium spp. Abdominal pain was the prominent complaint of infected individuals. Despite relatively low prevalence rates, the presence of C. cayetanensis and Cryptosporidium spp in Izmir province requires further assessments of intestinal parasites. Public health measures that may prevent the local risk factors of infection should be improved and implemented.