The present study was conducted to investigate the presence of Cryptosporidium spp. agents in cats from the Turkish Van Cat Shelter at YuzuncuYil University by a modified Ziehl-Neelsen staining method and nested PCR. Individual stool samples were obtained from 30 adult females, 30 adult males and 40 kittens - a total of 100 Van cats were analyzed in the study. A simplified formol-ether concentration method was applied to all samples. The samples were then examined microscopically by a modified Ziehl-Neelsen staining method. As a result of the staining, Cryptosporidium spp. oocysts were identified in stool samples of 3 kittens in the microscopic examination. After that, PCR and nested-PCR were conducted with suitable primers. Nested PCR identified 5 kittens (5%) as positive. As a result, it was concluded that nested PCR was a superior diagnostic method for Cryptosporidium diagnosis compared with staining methods and that infected cats could be a health hazard for other cats and individuals, since Cryptosporidium spp. agents infect via the faecal-oral route. Therefore, we believe it is necessary to raise the awareness of people in contact with cats.