The objective of this study was to evaluate associations between herd-level factors and the isolation of Salmonella in calves from dairy farms 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. Salmonella was isolated in fecal samples from 176 (3.8%) of 4673 preweaned calves with 40 (31.0%) of 129 farms having at least one positive calf sample over the course of the study. Multivariable logistic regression using the generalized estimating equations approach was used to evaluate risk factors for Salmonella shedding after adjustment for effects of herd size, season, state of origin and the multiple sampling occasions per herd. Factors retained in the final model that were associated with an increased odds for Salmonella shedding were lack of routine feeding of milk replacer containing antimicrobials to preweaned calves (OR=2.8, 95% CI: 1.4, 5.8), use of maternity housing as a hospital area for sick cows more than once a month (OR=2.1, 95% CI: 1.1, 4.0), and cow prevalence level by visit, categorized into the following four-levels: > or =20% (OR=11.6, 95% CI: 5.7, 23.7), 10-19.9% (OR=4.7, 95% CI: 2.0, 11.5), 0.1-9.9% (OR=3.6, 95% CI: 1.5, 8.7) and 0% (reference level). Herd size was not associated with Salmonella shedding in the final multivariable model.