Cryptosporidiosis is considered to be a widespread world zoonosis. The occurrence of Cryptosporidium species was investigated in Roma children in a district of Eastern Slovakia and, at the same time, also in children of non-Roma parents. In total, 103 children (54 boys and 49 girls) between 0 and 14 years of age were involved in this study. Fifty-three were Roma children and 50 children represented a non-Roma control group. Fecal samples were examined: immunologically [enzyme-linked immunosorbent assay (ELISA) test to prove antigen in the feces] and by molecular analysis [nested polymerase chain reaction (PCR)]. After the sequencing of the PCR, the products were identified as species of Cryptosporidium muris. Based on the results, the relative risk (RR) of the Cryptosporidium infection occurrence was calculated and we came to the conclusion that the risk of Cryptosporidium infection was almost 12 times higher in the Roma children compared to the non-Roma children.