Background Cases of cryptosporidiosis have not been officially reported in Estonia after the year 2000, and the disease appears to be either under-diagnosed or under-reported. Findings Based on a human case of cryptosporidiosis contracted during faecal sampling in dairy farms, cattle considered to be sources of infection were analysed for Cryptosporidium spp. by a modified Ziehl Neelsen technique and molecular typing. C. parvum subtype IIaA16G1R1 was detected from the human case and from calves from one of nine farms enrolled in the study providing strong circumstantial evidence of zoonotic transmission from calves to humans. Conclusion Cryptosporidiosis presents an occupational risk to people with cattle contact, and may also be a risk to the human population in general. Thus increased public and medical awareness is warranted.