Two hundred and forty kennel and privately owned dogs were tested for a molecular epidemiological study on Cryptosporidium infection. Genomic DNA was extracted from individual faecal samples. All the DNA extracts were analysed with a PCR assay specific for a approximately 400-bp fragment internal to the gene encoding for the Cryptosporidium oocyst wall protein. The prevalence was 3.3% and it was higher in kennel dogs and in dogs with gastrointestinal symptoms. Cryptosporidium parvum was detected by sequencing analysis in six kennel dogs and one privately owned dog, and Cryptosporidium canis was detected in one kennel dog. This is the first investigation on the prevalence of Cryptosporidium in Italian dogs and has pointed to the existence of genotypes that may be of public health significance.