To assess the importance of cattle as a source of human cryptosporidial infections in Slovenia, Cryptosporidium isolates from calves and humans with cryptosporidiosis were characterized genetically by direct DNA sequencing, targeting a variable region of the 60 subtypes', were identified, of which 7 were novel. In humans, C. hominis Ia (subtype IaA17R3) and Ib (IbA10G2) and Cryptosporidium parvum IIa (IIaA9G1R1, IIaA11G2R1, IIaA13R1, IIaA14G1R1, IIaA15G1R1, IIaA15G2R1, IIaA16G1R1, IIaA17G1R1 and IIaA19G1R1), IIc (IIcA5G3), and IIl (IIlA16R2) were recorded; this is the first record of the latter subtype in humans. In cattle, C. parvum IIa (IIaA13R1, IIaA15G2R1, IIaA16R1 and IIaA16G1R1) and IIl (IIlA16R2 and IIlA18R2) were recorded. Of the 15 subtypes identified, subtypes of C. parvum IIa were the most frequently encountered (>90%) in both humans and calves. The present findings suggest that zoonotic transmission plays an important role in sporadic human cryptosporidiosis in Slovenia.