Breast cancer has different molecular subtypes, which determine the prognosis and response to the treatment. CD133 is a marker for cancer stem cells in tumor microenvironment with diagnostic/therapeutic importance. The tumor associated macrophages (TAMs) interact with the cancer stem cells through the CXCR1 receptor. In this study, we wanted to investigate the expression of these markers in patients with different molecular subtypes, in order to detect pathophysiological mechanisms and new molecular targets for the prospective targeted therapies. In this study we hypothesized a difference in expression of these antigens among different subtypes. We investigated expression of antigens in breast cancer patients with luminal A (LA), luminal B (LB), HER2 overexpressing (HER2OE), triple negative (TN) subtypes (n=70) and control patients (n=10) without cancer diagnosis. We applied indirect immunohistochemistry and evaluated immunostaining. CD133 expression was at the periphery and CXCR1 expression was at the central area of the tumor. The cytoplasmic CXCR1, CD133 expressions and nuclear CD133 expression, which is prominent in the TN subtype, were observed in patients. There was a statistically significant difference between the groups for CD133 (p=0.004), CXCR1 (p=0.002) H-Score values and M2 macrophages/whole TAM ratios (p=0.022). Between the CD133 and CXCR1 H-scores, there was a weak positive correlation (r=0.249, p=0.035). This study showed the compartment specific expression of the CD133 and CXCR1 antigens in neoplastic cells. The use of CD133 as a stem cell marker may be limited to TN subtype, due to its heterogeneous expression.