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Abstract Background Hock lesions (HL) in dairy cows are a common animal welfare problem in modern dairy production with freestall housing systems, but there are no large-scale studies addressing its epidemiology in Sweden. The aims of this cross-sectional study were to investigate the prevalence of HL of different severity in 100 Swedish freestall dairy herds, and to identify cow- and herd-related risk factors. Associations between HL and mastitis as well as culling were also investigated. Results In total, 3217 cows from 99 herds were included in the statistical analyses. The overall cow prevalence of hair loss on the hock (mild HL) was 68% and the prevalence of ulceration or evident swelling of the hock, with or without hair loss, (severe HL) was 6%. The within-herd prevalence varied among herds, between 23 and 100% for mild HL, and between 0 and 32% for severe ones. Breed (higher risk for Swedish Holstein than for Swedish Red) and days in milk (higher risk at 181–305 days than at 0–90 days) were cow-related risk factors associated with both types of lesions, whereas higher parity and cleaner cows were associated only with increased risk of severe HL. A reduced risk for mild HL was seen in cows housed on mattresses compared to rubber mats, and in cows housed on peat compared to other bedding materials. Also, cows in herds with a high proportion of not yet inseminated heifers older than 17 months had a lower risk of mild HL than cows in herds with a low proportion. Risk for severe HL was lower when cubicles were of recommended width compared to under recommendation, for organic production compared to conventional, and when teat dip or no treatment after milking was used, compared to teat spray. For both mild and severe HL, herringbone milking parlors were associated with higher risk than tandem parlors. We found no significant associations between HL and mastitis or culling. Conclusions The prevalence of HL is high in Swedish dairy herds, although most lesions are mild. Several cow- and herd-related risk factors were identified and the results can be used to improve recommendations for the prevention of HL in Swedish freestall dairy herds.