Class-II human leukocyte antigens (HLA) present tumor antigenic peptides on the cell surface in order to be recognized by T lymphocytes. Thereby, these molecules can play an important role in the immune response to breast cancer tumor antigens. The aim of this study was to determine the relation between breast cancer and HLA class-II alleles in Turkey. The study groups consisted of 69 breast cancer patients and 45 healthy controls. Typing of HLA-DRB1 and HLA-DQB1 from DNA samples was performed by Sequence Specific Oligonucletide Hybridisation. Significant negative correlations were observed between HLA-DRB1*03 and HLA-DQB1*02 alleles and breast cancer (p1 = 0.019; p2 = 0.019) and also between HLA-DQB1*02 allele and postmenopausal breast cancer (P = 0.022) and c-erb-B2 positivity (P = 0.038). Furthermore, there was a significant positive correlation between HLA-DRB1*13 and HLA-DQB1*06 alleles and progesteron receptor positivity (p1 = 0.012; p2 = 0.001); and a significant negative correlation between HLA-DQB1*03 allele and progesteron receptor positivity (P = 0.009) in breast cancer. Additionally, another significant positive correlation was seen between HLA-DRB1*04 allele and c-erb-B2 positivity (P = 0.036). As a result, while HLA-DRB1*03, HLA-DQB1*02, HLA-DRB1*13, and HLA-DQB1*06 alleles were found to be involved in protectiveness against breast cancer and good prognosis; HLA-DQB1*03 and HLA-DRB1*04 alleles were found to be involved in poor prognosis. In conclusion, by determining allele types showing predisposition to breast cancer, a systematical screening and follow up systems can be developed for patients who are at high risk.