Cryptosporidiosis is recognized as being a significant cause of gastrointestinal illness due to its wide range of vertebrate hosts, including humans. Infection with Cryptosporidium spp. is especially common in young domestic ruminants (calves, lambs and goat kids) and has been associated with economic losses worldwide. In contrast to cattle, to date, detailed studies on Cryptosporidium infections in sheep from Europe are still limited; thus, their importance as reservoirs of Cryptosporidium species with implications on animal and public health still needs to be clarified. This study evaluates the prevalence and zoonotic potential of Cryptosporidium spp. in sheep farms in Italy. A total of 915 individual faecal samples divided into three different animal categories were collected from 61 sheep farms. Each sample was examined by microscopy of faecal smears stained by modified Ziehl-Neelsen and by biomolecular techniques. Cryptosporidium oocysts were detected in 10.1% of the animals examined and in 34.4% of the farms. The prevalence of Cryptosporidium spp. was significantly higher (χ2 = 51.854; P < 0.001) in diarrhoeic samples than in pasty or normal faeces. Genotype analyses showed the presence of two Cryptosporidium species: C. parvum and C. ubiquitum. Subtyping analysis of C. parvum isolates revealed the presence of subtypes IIa15G2R1 and IIdA20G1 and of subtype XIIa for C. ubiquitum. These findings have public health implications since both Cryptosporidium species identified are considered zoonotic, and C. parvum is the second-most common Cryptosporidium species infecting humans. Our data reveal that lambs, especially those excreting diarrhoeic faeces, may be important reservoirs of Cryptosporidium. We also highlight the need to establish adequate control and monitoring programmes for the control of this infection in sheep farms primarily through coprological monitoring.