A cross-sectional study was designed to investigate the prevalence and risk factors for Cryptosporidium infection in young calves. Forty-one farms in a discrete, densely farmed 100 km2 area of North West England were visited over a 3-week period and 215 faecal samples were collected from young calves. Farms were not selected on the basis of existing scour problems. At the time of sampling, several investigator-observed variables were recorded at the pen, animal and stool levels. Samples were screened and 60/215 were confirmed as positive by PCR of the 18S rRNA gene. Risk factors for infection were explored using multilevel multivariable logistic regression with farm as a random effect. Age was significant in the final model, with a higher risk of infection in calves aged 8-21 days, when compared to those aged 0-7 days. The depth of the bedding was also significant in the final model, with calves housed in bedding 11-15 cm deep being at lower risk of infection than those on beds 0-5 cm deep. Consistency of the faeces was highly correlated with age and colour of the faeces and was not significantly associated with infection when these variables, and clustering at farm-level, were accounted for. This is interesting as Cryptosporidium is considered to be a primary enteropathogen. The results suggest that intervention strategies should be targeted at calves under 21 days old. These animals represent a significant reservoir of infection on the farm and may also pose a risk to public health, assuming that the species and genotypes shed are zoonotic pathogens.