A longitudinal study was undertaken to determine the spread of naturally acquired Giardia and Cryptosporidium in dairy cattle in Western Australia. Samples were collected weekly from birth to weaning, and only calves that were sampled four or more times were included in the analysis. It was found that calves rapidly acquire infections with Cryptosporidium parvum and Giardia, with Cryptosporidium being the first to appear within 1-3 weeks after birth whereas Giardia was most prevalent in calves 4-7 weeks of age. Cryptosporidium and Giardia were detected in 48 and 89% of sampled calves, respectively. No significant association was observed in the present study between parasite occurrence and season or management practices (housing), and calf-to-calf contact appears to be the most likely source of transmission. Molecular characterization of isolates of Giardia and C. parvum recovered from calves demonstrated that only the occurrence Cryptosporidium represents a public health risk in terms of the potential for zoonotic transmission.