Abstract: The polymorphism in the bovine κ-casein (κ-CN) and β-lactoglobulin (β-LG) genes were analyzed for DNA sequence variants using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique in Iranian Holstein population to find association between the genotypes and milk traits as well as somatic cell score. To this purpose, 2537 test day records of one hundred thirty nine dairy cows were entered in a repeated generalized mixed model. The frequencies of alleles A and B were estimated as 0.81, 0.19 and 0.57, 043 for κ-CN and β-LG loci, respectively. The results of association analysis by the mixed model revealed a significant positive relationship of κ-CN genotype AA on milk yield (p≤0.04). These analyses did not reveal a significant association of κ-CN genotypes with fat percent and SCS traits. In the case of β-LG locus statistical analysis showed a strong relationship between BB genotype and protein percentage (p≤0.007) comparing to the other genotypes. These results did not reveal a significant association of β-LG genotypes with milk yield, milk fat percentage and SCS in studied animals. A tendency to being significant was however observed for β-LG genotype AA (p<0.12) with the SCS trait. Because of the lack of consistency among results of similar studies, we suggest further investigations to determine the precise nature of these associations with the milk proteins to be performed based on haplotypes.