Accumulative evidences have shown that certain HLA loci are associated with alopecia areata (AA), but with existing differences in ethnic distribution. No report has ever been published about this in Chinese Hans. To investigate whether HLA-DQA1 and DQB1 alleles are associated with AA, and the correlation of the HLA profile with age of onset, severity, duration of current attack, recurrence and family history of AA in Chinese Hans. The polymerase chain reaction-sequence-specific primer (PCR-SSP) method was used to analyze the distribution of HLA-DQA1 and DQB1 alleles in 192 patients with AA and 273 healthy controls in Chinese Hans. The significant increased frequencies of HLA-DQA1*0104 (OR=3.38, P(c)<0.001), HLA-DQB1*0604 (OR=5.17, P(c)=0.006) and HLA-DQA1*0606 (OR=3.73, P(c)<0.001) were observed in patients compared with controls. The DQA1*0104-DQB1*0604, DQA1*0104-DQB1*0606, and DQA1*0302-DQB1*0606 were found as high-risk haplotypes in developing AA in this study. HLA-DQA1*0104 (OR=5.31, P(c)<0.001) and -DQB1*0604 (OR=5.56, P(c)=0.015) were more prevalent only in AA patients with long duration than controls. The frequencies of HLA-DQB1*0604 (OR=5.42, P(c)=0.009) and -DQB1*0606 (OR=4.11, P(c)<0.001) were obviously increased in patients less than 50% scalp hair loss. No locus was merely associated with early onset, severe involvement, recurrence and a positive family history of AA. This study demonstrated the positive association of HLA-DQA1 and DQB1 alleles and haplotypes with AA. There may be differences in genetic background in patients with different duration.