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India is the highest milk producer of the world and crossbreeding to augment genetic potential of native breeds, has played an important role to achieve this feat. The present study with five microsatellite DNA loci BM1818, BM1443, BM1905, BM1258 and MB026 associated with Somatic Cell Score (SCS) and milk production, was aimed at finding variation in 76 crossbred cows. PCR amplified products were resolved on MetaPhore® agrose. The number of alleles for BM1443, BM1905, BM1258 and MB026 were found to be 7 each while it was 8 in BM1818. The size of alleles ranges from 149-186 bp for BM1443, 178-204 bp for BM1905, 208-252 bp for MB026 and 252-296 bp for BM1818. The data on polymorphism information content, heterozygosity, number of effective alleles of these short tandem repeat loci shows that BM1443 was having lowest and BM1818 was having maximum variability. Microsatellite BM1818 was not found to be associated with SCS in this population. Means of SCS of genotypes 178/192 and 188/188 for marker BM1905, genotypes 228/252 and 238/ 252 for marker MB026, genotype 120/110 for marker BM1258 and genotypes 182/154 and 178/154 for marker BM1443 were found to be higher. Only two markers viz. BM1818 and BM1443 was found to be significantly associated with 305 days milk yield. [ABSTRACT FROM AUTHOR]