Recently, the Cryptosporidium sp. rabbit genotype has emerged as a human pathogen (Chalmers et al., 2009). Cryptosporidium is a protozoan parasite which causes the gastrointestinal disease cryptosporidiosis. This is characterised mainly by watery diarrhoea and abdominal pain and lasting for a couple of weeks. In immunocompromised individuals, the disease can be more severe and even fatal. Currently, there are 20 valid Cryptosporidium species and numerous “genotypes”, infecting in total over 150 host species. The major pathogens are Cryptosporidium hominis and Cryptosporidium parvum in humans and C. parvum in young animals.