The genotypes and protein polymorphisms of milk epithelial mucin (MUC1) were analyzed by touch-down PCR and SDS-PAGE respectively using blood samples and milk collected from 50 lactating yaks. A total of seven alleles were revealed, namely A, B, C, D, E, F, and G, and the corresponding number of repetitive units of variable number tandem repeat (VNTR) in MUC1 gene were 21, 20, 19, 18, 17, 16, and 15, respectively. Fifteen genotypes of MUC1 were observed in yaks. The genotypes of MUC1 gene matched completely to the phenotypes of milk MUC1 in each individual. This study demonstrated that the yak MUC1 exhibits abundant polymorphisms in both its gene and protein, and the polymorphisms are due to the expression of VNTR in MUC1 gene. The possible cluster of the VNTR was also discussed in different ruminants.