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Based on the reports, few HLA class II alleles are associated with susceptibility or protection in breast cancer. Here we investigate the association between HLA class II alleles and breast cancer in Iranian women. 100 patients with pathologically proven breast cancer who referred to Cancer Institute were randomly selected and compared with a group of 80 healthy blood donor subjects. The patients were studied in two groups, group 1 includes patients aging 40 years or younger and group 2 include patients aging over 40 years. HLA class II alleles were determined by amplification of DNA followed by HLA-typing using sequence-specific primer (SSP) for each allele. In group 1, the most frequent alleles were HLA-DQA1*0301 (P = 0.002, OR = 3.3) and HLA-DQB1*0302 (P = 0.04, OR = 2.8). In group 2, the following alleles increased significantly than those in controls including HLA-DQA1*0301 (P …