The public health risks associated with dairy farming intensification are an emerging concern. We examine the association between dairy cattle density and cryptosporidiosis risk in children <5 years old in New Zealand from 1997 to 2008, a period of rapid intensification of the dairy industry. Multi-level Poisson regression was used to model reported cryptosporidiosis (N = 3869 cases) incidence in relation to dairy cattle densities across urban and rural areas separately, after controlling for microbiological quality of public drinking water supplies and neighbourhood socio-economic factors using the Census Area Unit of residence. Within urban areas, the risk of cryptosporidiosis in children less than 5 years old was significantly, positively associated with medium and high dairy cattle density IRR 1.3 (95% CI 1.2, 1.5) and 1.5 (95% CI 1.2, 1.9) respectively, when compared to areas with no dairy cattle. Within rural areas, the incidence risk of cryptosporidiosis in children less than 5 years old were significantly, positively associated with medium and high dairy cattle density: IRR 1.7 (95% CI 1.3, 2.3) and 2.0 (95% CI 1.5, 2.8) respectively, when compared to areas with no dairy cattle. These results have public health implications for children living on and in proximity to intensively stocked dairy cattle farms.