Breast cancer (BC) which is accepted as the most common invasive cancer among women, can be caused by many factors. Fetal microchimerism (FMc) known as the long-term persistence of small numbers of fetus-derived allogeneic cells in mother is a potential contributor or a protective factor in some diseases, including breast cancer. The presence of Y chromosome and X-chromosome aneuploidies have been associated with BC. We investigated the possible roles of microchimeric cells (McCs) in BC development by detecting the presence of Y chromosome and X-chromosome aneuploidies in a selected group of patients. For this purpose, the fluorescent in situ hybridization (FISH) technique was applied to malignant tumor tissues of 49 BC patients and blood samples of 32 healthy controls. While fetal McCs (FMcCs) were found in malignant tumor tissues of 10 (20.41%) BC patients, all of the healthy controls showed no detectable Y chromosome signals in their blood (p=0.000). Besides, it was found that X-chromosome polysomies increased in BC patients with raised age (p=0.020) and who breastfed their children (0.039), and X-chromosome monosomies were increased in patients who delivered a son at their first pregnancy (p=0.016). On the other hand, X-chromosome monosomies was found significantly higher in early-stage tumors (I and II) than in advanced-stage tumors (III and IV) (p=0.020). FMcCs was present in breast tumor of women who have a male child and, probably allogeneic maternal immune reaction may have led to cancer development in those cases. The presence of FMcCs in breast tissue may be protecting women from cancer for a period of time after delivery, but have the potential to cause cancer in the later period. Detection of X-chromosome aneuploidies in BC patients with raised age and X-chromosome monosomies in the early stages of BC can be used as early markers in the diagnosis of BC.