The objective of this study was to evaluate associations between herd characteristics and the isolation of Salmonella from dairy cows in Minnesota, Wisconsin, Michigan, and New York. Study farms were 129 conventional and organic farms enrolled without regard to previous history of Salmonella infection. Herds were sampled at 2-month intervals over a 1-year period. This is the largest study to date on Salmonella shedding in dairy cows and the only study evaluating herd-level risk factors using longitudinal sampling to characterize Salmonella shedding on dairy farms. Salmonella was isolated in fecal samples from 1026 (4.9%) of 20,089 cows. Over the course of the study, 113 (87.6%) of 129 farms had at least one positive cow sample. Multi-variable logistic regression using the generalized estimating equations approach was used to test the association between herd-level risk factors and the dependent variable of within-herd prevalence by visit (number of Salmonella-positive cows/number of cows sampled) after adjustment for effects of herd size, season, state of origin, and the multiple sampling occasions per herd. Factors retained in the final model included lack of use of tiestall or stanchion facilities to house lactating cows (OR=1.9; 95% CI: 1.1-3.3), not storing all purchased concentrate or protein feeds in an enclosed building (OR=2.5; 95% CI: 1.3-4.9), not using monensin in weaned calf or bred heifer diets (OR=3.2; 95% CI: 2.0-5.4), access of lactating or dry cows to surface water (e.g., lake, pond, river, or stream) (OR=2.3; 95% CI: 1.3-3.9), disposal of manure in liquid form (slurry or irrigation, as opposed to disposal of manure by broadcast/solid spreader only) on owned or rented land (OR=1.8; 95% CI: 1.3-3.9), and cows eating or grazing of roughage from fields where manure was applied in solid or liquid form and not plowed under during the same growing season (OR=1.8; 95% CI: 1.0-3.0). A seasonal association was also present as cows were more likely to be Salmonella-positive in summer, spring, and fall compared to winter. Herd size was not associated with Salmonella shedding in the final multi-variable model. The herd-level risk factors identified in this study could potentially be implemented in Salmonella control programs on dairy farms.