This study was conducted to investigate the prevalence of Cryptosporidium spp. in children (n=760) with diarrhea aged 1 month to 13 years, living in urban areas (n=234), rural areas (n=394) and refugee camps (n=132). Samples were collected, stained by modified acid fast stain, and examined microscopically for oocysts. The overall prevalence was 11.6% (88/760). The prevalence was higher in refugee camps at 12.9% (17/132) and in rural areas at 12.2% (48/394) as compared to 9.8% (23/234) in urban areas. According to age, the prevalence in age group I (<5 years) was significantly high (P<0.05) at 14.4% (67/464) as compared to 7.7% (15/195) in age group II (5-10 years) and 5.9% (6/101) in age group III (10-15 years). Our findings indicate that the prevalence of Cryptosporidium spp. is high when compared to that in developed countries.