The study investigates farms suspected of being sources of zoonotic human cryptosporidiosis. A variety of implicated farm animal species were sampled and tested to detect Cryptosporidium oocysts and investigate genetic linkage with human patients. Risk factor information was collected from each farm and analysed by multivariable logistic regression to detect significant associations between factors and Cryptosporidium in animals. The results showed that average sample prevalence of Cryptosporidium infection was highest in cattle, sheep and pigs ( approximately 40-50%), in the mid-range in goats and horses (20-25%) and lowest in rabbits/guinea pigs, chickens and other birds ( approximately 4-7%). A single sample from a farm dog was also positive. Cryptosporidium parvum, which has zoonotic potential, was the commonest species and was most likely to be present in cattle and, to a lesser extent, in sheep. In particular, young calves and lambs shed C. parvum and this finding was corroborated in a statistical model which demonstrated that samples from groups of preweaned animals were 11 times, and immature animal groups six times, more likely to be positive than groups of adult animals, and that samples from a farm with a cattle enterprise were twice as likely to be positive than farms without a cattle enterprise. On seven out of eight farms, at least one C. parvum isolate from an animal sample was indistinguishable at the gp60 locus from those found in the human patients, indicating that farm animals are a likely source of infection for humans.