Objective To study the distribution of human papilloma virus(HPV)subtypes in Uyghur people from the high risk region of cervical cancer in Xinjiang. Methods 21 subtypes of HPV from 400 cases of men's swabs of penile and 400 cases of women's cervix swabs were detected, using flow-through hybridization and gene chip technology. Results(1)The positive rate of HPV among the 400 women cases was 14.25% ,with HPV16 the most common type. In women whose HPV was positive, the positive rate of HPV16 was 66.67%. The ranking of frequencies on the HPV subtypes in women were: HPV 16, 58,39, 18,33,52,43,66, CP8304, HPV6 and 11.(2)Among the 400 male cases, the positive rate of HPV was 8.00%, with HPV16 the most common type. In men whose HPV was positive, the rate of HPV16 was 44.44%. The ranking of HPV subtypes in men were HPV16, 43, 33, 39, 6(HPV39 and 6 are equivalent)and 53.(3)Both wives and husbands were infected by different subtypes of HPV, the positive rate was relatively low among men whose wife's HPV were positive. However, the HPV positive rate was relatively low among women whose husband's HPV were positive. The concordance infection rate of women and men were 7.02% and the concordance infection rate of men and women were 9.38%. Conclusion The HPV positive rates were relatively low in both men and women living in the region with high risk of cervical cancer in Xinjiang. However, the positive rate of high risk types HPV and HPVI6 in both men and women were relatively high. Uyghur men seemed to have played a certain role related to the carcinogenensis of cervical cancer. HPV16 was the main type in both men and women in Xinjiang.