OBJECTIVE Determine the prevalence of the major enteric pathogens in dairy and dairy beef calves with diarrhoea in Australia. METHODS Cross-sectional study. METHODS Faecal samples from 84 Australian dairy and dairy beef properties (597 samples) were screened for rotavirus and coronavirus using real-time reverse transcription polymerase chain reaction, for Salmonella spp. using selective enrichment faecal culture, and for enterotoxigenic Escherichia coli (K99) and Cryptosporidium parvum using a commercial enzyme-linked immunosorbent assay. A logistic regression with random effects model was used to compare prevalence of pathogens in dairy and dairy beef operations. RESULTS Enteric pathogens were isolated from 97.6% of outbreaks and 95.0% of samples. Rotavirus was the most common pathogen identified (477/597, 79.9%) followed by C. parvum (349/597, 58.5%), Salmonella spp. (142/597, 23.8%), coronavirus (129/597, 21.6%) and E. coli K99 (104/597, 17.4%). Multiple pathogens were identified on 96.4% of farms and from 71.0% of samples. Samples from dairy beef properties were more likely to have multiple pathogens than dairy properties (P < 0.05), whereas rotavirus and Salmonella spp. were more likely to be identified in samples collected from dairy beef than dairy properties (P < 0.05). CONCLUSIONS Most outbreaks of calf diarrhoea in dairy and dairy beef operations involve multiple pathogens. Rotavirus and C. parvum were the most frequently identified pathogens across production systems. Salmonella spp. and rotavirus were more frequently identified in dairy beef operations.