To display the association between the apolipoprotein E (APOE) genotypes and breast cancer patients, a cross sectional study including 291 patients and 148 controls was performed. The APOE genotypes were measured in all participants, and the pathological diagnosis, estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 (HER-2) among breast cancer patients were collected. The results showed the APOE allele frequency in breast cancer patients was 11.7% epsilon2 carriers, 74.6% epsilon3 carriers and 13.7% epsilon4 carriers, and there was no significant difference when they were compared with those of the control group (15.5% epsilon2 carriers, 74.3% epsilon3 carriers and 10.1% epsilon4 carriers; p=0.342). Among the patients in pre-menopause, showed a higher frequency of epsilon2 carriers had the cancer site on the left than that of the epsilon3 carriers (78.6% versus 40.3%; p=0.019). Among breast cancer patients, there was no significant association between the APOE genotypes and menopausal status, pathological diagnosis, estrogen receptor, progesterone receptor, and HER-2. Our findings demonstrated that the APOE genotypes were not associated with breast cancer patients, and epsilon2 allele tended to induce breast cancer on the left site among those patients in pre-menopause.