382 yak cows were examined for milk yield, fat, protein and lactose contents. Six polymorphic loci, alphas1-CN, kappa-CN, beta-CN, beta-Lg, alpha-La and MUC-1, were scored by PAGE electrophoresis for each individual. The values of milk yield, fat, protein and lactose content were 247.13 kg, 5.81%, 5.18% and 4.93%, respectively. Based on the 6 polymorphism loci, the average heterozygosity of the yak population was 0.1794. Calculated by the marker-based method, heritability estimates for milk yield, fat, protein and lactose contents were 0.353 +/- 0.093, 0.316 +/- 0.101, 0.415 +/- 0.098 and 0.481 +/- 0.035, respectively. The relatively high or medium heritability of these traits indicate that it is feasible to rely directly on them in breeding for the improvement in a relatively short period. The significant linear regression between heterozygosity and fat percentage with a positive slope (R = 0.0420) indicated that inbreeding affected milk fat content in this population.