Juvenile hedgehogs having insufficient body weight are often brought for overwintering to hedgehog rehabilitation centres. Faecal samples of juvenile hedgehogs and overwintering hedgehogs (n=188) collected prior to releasing them back into the wilderness were examined for the presence of Cryptosporidium coproantigen and oocysts. Altogether 56 (29.8%) submitted samples were positive for coproantigen. Forty-five (39.5%, n=114) of the positive samples originated from newly rescued hedgehogs, while 11 (14.8%, n=74) positive samples were from animals that spent several months at the station. Fifteen samples subjected to PCR-RFLP analysis on the partial 18S rRNA locus suggested the presence of C. parvum. Multilocus sequence typing on partial 60 kDa glycoprotein gene, 18S rRNA, actin gene, 70 kDa heat shock protein gene sequences revealed 3 different subtype families: IIa, IIc and a new, proposed as VIIa subtype family. Cryptosporidium sp. genotype belonging to VIIa subtype family is closely related to C. parvum but is genetically distinct being probably a hedgehog-specific Cryptosporidium sp. genotype with unknown zoonotical potential. Hedgehogs excreting Cryptosporidium oocysts represent a potential source for human infections, but also an anthroponotic nature of the IIc subtype family should be reviewed.