SummaryBovine respiratory disease (BRD) is considered one of the most economically important diseases in the cattle industry. Ultimately, the selection of cattle that are less susceptible to disease will allow producers to reduce the prevalence of BRD and lessen its economic impact. The objective of this study was to validate previously identified loci associated with susceptibility to BRD in an independent population of 140 pre‐weaned Holstein calves from Wisconsin (WI). Using the McGuirk health scoring system, calves were classified as either clinically affected with BRD (n = 35) or healthy (n = 105). Additive genotypic tests were performed for genomic regions previously associated with susceptibility to BRD in calves from California (CA) and New Mexico (NM). Using this method, 4 loci (P < 0.01) consisting of 10 SNP were validated in the WI population, including 2 loci from CA, 1 locus from NM, and 1 locus from a combined CA + NM population. Most of the positional candidate genes and transcription factor binding site motifs associated with these loci have functions related to innate and adaptive immune responses. The validation of loci associated with susceptibility to BRD in independent populations allows producers to more reliably select cattle that are less susceptible to BRD, improving animal welfare, decreasing the annual revenue losses, and lowering the prevalence of the disease.