Genetic diversity in candidate genes for fitness and production traits was explored in three populations of dairy cattle. The study focused on adipokines, including leptin (LEP), tumor necrosis factor alpha (TNF), interleukin-8 (IL8) and interleukin-10 (IL10) as candidate genes. The three populations of interest included young Jersey and Holstein (modern Holstein) sires, and Holstein sires born prior to 1970 (traditional Holstein). Pools of DNA representing each sire group were used as template to generate PCR products for sequencing and identification of single nucleotide polymorphisms (SNP). Sequences of PCR products were assembled and SNPs identified using Sequencher 4.5 software. One SNP representing each gene and a previously reported SNP in LEP were selected for genotyping across all bulls. A multiplexed genotyping assay was developed using the ABI PRISM SNaPshot Multiplex Kit. Allele and genotypic frequencies were determined for each sire group, and genotypic frequencies were in agreement with Hardy-Weinberg equilibrium. Allele frequencies were compared among sire groups using the chi-square test. A significant difference between Jersey and Holstein was observed for all genes, and modern and traditional Holstein groups differed for the previously described LEP and IL10 SNP. Although allele frequency differences between modern and traditional Holsteins may reflect the effect of selection pressure for production traits on these genomic regions, random genetic drift or sampling bias could also have contributed to the observed differences.