Cryptosporidiosis is a zoonotic disease that occurs acutely or chronically in young or immune-compromised animals and humans, caused by Cryptosporidium species. Cryptosporidium is recognized as one of the major enteropathogens associated with neonatal diarrhea in ruminants. The aim of this study is to determine the prevalence of Cryptosporidium spp. in lambs in Siirt province using microscopic and molecular methods. The fecal materials of the study collected from 194 randomly selected lambs of different sexes, up to 4 weeks of age, in various farms. As a result of microscopic examination, Cryptosporidium spp. oocysts were found in 54 (27.84%) of 194 samples, while specific bands were obtained in 63 (32.47%) samples as a result of Nested PCR analysis. A statistically significant relationship was found between lambs with and without diarrhea (P<0.001) while no statistically significant relationship was found between age groups, gender, and locations (P>0.05). In conclusion, the data obtained from this study revealed that Cryptosporidium infection is present in Siirt province, and Cryptosporidium spp. should be considered as one of the agents in the etiology of neonatal diarrhea in lambs.