The prevalence of Cryptosporidium spp. in diarrheic immunocompetent children living in Switzerland was 5.5% (15 of 273). Infection rates increased significantly with age. Anthroponotic Cryptosporidium hominis was identified in 11 children, 9 with a travel history. The zoonotic Cryptosporidium parvum bovine genotype was identified in 3 children (2 without travel history). Hence transmission of Cryptosporidium spp. is primarily of anthroponotic nature in the study area.