Background: Globally, breast cancer is the second leading cause of death among women in Iraq. Several genetic and environmental factors are associated with the occurrence of the breast cancer. Methods: The aim of this study was to isolate and identify aerobic bacteria from breast tumors. Total 100 samples (50 swabs and 50 biopsies) were collected aseptically from benign and malignant breast tumor specimens of Iraqi patients admitted to Baghdad Medical University Hospital. Bacteria were identified using traditional diagnostic methods, API® Staph as well as VITEK® Card. Furthermore, using species-specific primers, the polymerase chain reaction (PCR) assay followed by electrophoresis verified the most common isolates. Results: Among the isolated bacteria, Staphylococcus epidermidis comprised the highest incidence rate (50.6%) of the 77 culture positive swabs and biopsies. Interestingly, the number of S. epidermidis isolates was 27 out of 50 (54%) in malignant tumors and 12 out of 27 (44.4%) in benign samples. These bacteria were further verified by amplifying recN, which encodes a recombination/repair protein. On disc diffusion antimicrobial susceptibility test, most of the isolated bacteria showed methicillin resistance which was confirmed by amplifying the mecA gene using PCR. Conclusions: These data suggest that S. epidermidis might play an important role in breast carcinogenesis.