Gao, J., Jiang, Z.-R., Liu, X., Zhao, Y.-H., Huang, L., Peng, H.-J., Zedan, D., Jin, S.-Y. and Zheng, Y.-C. 2014. Comparison of MUC1 variable number tandem repeat polymorphisms in three yak breeds/populations. Can. J. Anim. Sci. 94: 411-416. The objective of this study was to compare the MUC1 variable number tandem repeat polymorphisms with adjacent distribution regions in three yak (Bos grunniens) breeds/populations. A total of 215 yaks of three yak breeds/populations (Maiwa yak breed, Jiulong yak breed and Changtai yak population) were surveyed by the polymorphisms of Mucin 1 gene (MUC1). Six MUC1 alleles (B, C, D, F, G and H) forming 16 genotypes were identified. Cloning and sequencing of these alleles demonstrated that they differed in the numbers of variable number tandem repeats (VNTR) units ranging from 14 to 20, and allele H (14 VNTR units) was a new allele in yaks and observed only in Maiwa yak with a very low frequency. Cluster analysis based on MUC1 polymorphisms suggested that Changtai yak population has a closer association with Maiwa yak breed than with the Jiulong yak breed, and may represent an independent yak breed/population. These results provided useful genetic information on the three yak breeds/populations and could be used in yak breeding practice.