Abstract Worldwide, there is considerable between-herd variation within individual foot lesion prevalence studies. This variation suggests that herd-level risk factors are important from a prevention perspective. The objective was to determine the effect of selected risk factors on the prevalence of 7 foot lesions in both tie-stall and free-stall housing systems. As part of a cross-sectional foot lesion study 5 hoof trimmers recorded lesions for all cows that were foot trimmed in a herd. In addition, they completed a risk factor questionnaire for each herd. The impact of specific risk factors was evaluated using separate multi-variable models for both free-stall and tie-stall herds. The lesions evaluated were digital dermatitis, sole ulcer, sole hemorrhage, heel horn erosion, white line separations, white line abscess, and interdigital fibroma. Model types were selected based on herd-level lesion distribution. Detrimental risk factors identified in free-stall housing included increased alley scraping frequency (2.2- to 2.4-fold for sole ulcers) and trimming in summer or fall (−0.2-fold vs. spring and winter for digital dermatitis). Protective risk factors in free stalls included intermediate bedding depth (0.4-fold for 2.5 to 7.5cm vs. more or less bedding for interdigital fibroma) and trimming heifers before calving (0.1-fold for white line abscess). In tie-stall herds no protective risk factors were identified. Detrimental risk factors for lesions in tie stalls included year-round access to outside areas (2.1-fold increase in digital dermatitis, 3.5-fold for white line separation, and 7.0-fold for interdigital fibroma vs. no or only seasonal exercise access), routine spraying of feet (2.0-fold increase in digital dermatitis), larger herds (3.0-fold increase in interdigital fibroma vs. <41 cow herds), and the use of wood bedding material (6.5-fold vs. straw bedding for interdigital fibroma). The risk factors identified need further evaluation to determine the temporal relationships, as well as whether the relationships with foot lesions are causal.