Several breeds of buffalo and cattle in Pakistan show mark differences in the milk yield. These animals are in a range of high milk producer to low. A proportion of these differences are explained by the animal genetic make up. In the earlier studies, a number of DNA polymorphisms have been reported in candidate genes. Among these few of candidate genes studied in the present study, are bovine growth hormone (bGH), kappa- casein (k-CN) and beta-lactoglobulin (B-LG) genes using PCR-RFLP methodology. Two genetic variants (A and B) and three genotypes AA, AB and BB have been identified. The genotyping of bovine growth hormone (bGH), kappa casein (k-CN) and beta- lactoglobulin (β-LG) alleles is of practical importance since bGH L, k-CN A & B and β- LG B alleles were found to be correlated with commercially valuable parameters. Genotype information on 366 animals from four breeds including one buffalo and three cattle breeds of Pakistan regarding polymorphisms located in the candidate genes was compared to literature reports. The results from frequency analysis revealed minor deviations from previous reports. Allele frequencies were calculated by gene counting methodology which shows the high prevalence of bGH genotype LL among cattle, while few animals had the LV variant and there was no VV variant was found. A Chi-Square test analysis of studied population of Pakistani cattle for bGH gene indicated that the studied population was in Hardy Weinberg equilibrium. Among cattle two alleles A and B in two genotypic forms AA and AB were found for κ-CN gene fragment. The frequency of allele A was found to be significantly higher in cattle whereas AB genotype was more frequent in Sahiwal cattle. No BB genotype was detected in any of these cattle. The Chi-Square test revealed that observed frequencies and those expected under Hary- Weinberg were not significant at (P< 0.05), suggesting that Cholistani and Red Sindhi population was in equilibrium for k-CN locus, while animals of Sahiwal cattle were not in Hary-Weinberg equilibrium. Analysis of β-LG gene, genotypes AA and BB were detected and no AB genotype was found in the tested animals of Nili-Ravi buffaloes while the frequency of AA genotype was higher. In cattle observed genotypes were AB and BB and the frequency of β-LG allele B was significantly higher in the analyzed animals of three cattle breeds. However, the important thing is the homozygosity found in Nili-Ravi buffaloes for bGH and κ-CN genes and this could be due to the loss of genetic variability among the studied population. Nucleotide sequencing from Nili-Ravi buffaloes shows maximum homology with Bubalus bubalis and Bos taurus breeds. On comparison of amplified gene sequence of Nili-Ravi buffaloes with Bubalus bubalis and Bos taurus breeds show variation at several sites. Thus results show that the PCR-RFLP analysis is easy, cost effective method which permits easy characterization of bGH, κ-CN and β-LG genes even in the absence of their expression. This will facilitates the selective breeding programs aimed at increasing the frequency of desirable alleles.