Breast cancer is the most prevalent malignancy in women throughout the world. Similar to other cancers, a strong relationship between breast cancer and environmental factors such as infectious agents has been reported. Toxoplasma gondii is a protozoan parasite which may play a role in cancer induction. The present study aimed to investigate a possible association between a history of T. gondii infection and breast cancer by detecting T. gondii DNA in malignant and non-malignant breast and lymph nodes tissues from breast cancer patients with latent toxoplasmosis. Formalin-fixed, paraffin-embedded (FFPE) tissue blocks from malignant/non-malignant breast and lymph nodes were obtained from twenty-nine breast cancer patients who were positive for anti-Toxoplasma antibodies (IgG). FFPE tissue blocks were deparaffinized by hot water method, and DNA was extracted. A conventional PCR analysis was performed to amplify partial regions of T. gondii B1 and REP-529 genes. Ninety-three samples from 29 patients were examined. All patients were negative for anti-T. gondii antibodies (IgM). T. gondii DNA was detected in 3 (10.3%) patients by PCR analysis of either B1 or REP-529 genes. These include two malignant breast and one normal lymph node samples. Sequence analysis of these genes showed a good similarity with previously published B1 and REP-529 sequences of T. gondii in NCBI GenBank. This study did not find any association between T. gondii infection and breast cancer. Furthermore, it is the first molecular identification of T. gondii in FFPE tissue samples obtained from breast cancer patients.