This study aimed to determined the expression levels of cancer stem cells (CSCs) markers OCT3/4, ALDH-1, CD44 and ABCG2 in addition to the matrix metalloproteinase (MMPs) such as MMP2 and MMP9 in Iraqi women with stage II-III breast cancer. Sixty four malignant breast cancer tissues and 21 corresponding benign tumor tissues were obtained from women with breast tumors admitted to the Alkarama Hospital in Baghdad, Iraq, during the period from June 2013 to April 2014.The patients enrolled in this study were diagnosed as stages II-III of breast cancer (60.9 % of cases were stage II and stage III represented 39.1%). Means age of patients was 64 years (range 36 to 77 years). In this study, the expression levels of CSCs as well as MMP2 and MMP9 were examined by using real-time PCR technique and immunohistochemistry. Results showed that there is a significant increase in the expression levels of OCT3/4, ALDH-1, CD44 and ABCG2 in the stage II breast cancer tissues (P=0.043, 0.015, 0.028 and 0.008,) and in stage III (0.004, 0.0045, 0.008 and 0.0001, respectively) as compared to that in benign tumors. MMP2 and MMP9 were high expressed in breast cancer stage II (p=0.0001 and 0.03), and in stage III (P=0.0001 and 0.001, respectively) as compared to benign tumor tissues. In addition, there is a significant variation between the MMP2 and MMP9 expression levels in stage II and stage III breast cancer (P=0.03 and 0.003, respectively). Immunostaining revealed that OCT3/4, ALDH-1, CD44 and ABCG2 were expressed in (81.2%, 67.2%, 57.8% and 82.8%, respectively) in cancerous tissues compared with (14.3%, 28.6%, 33.3% and 19%) in benign tumor tissues. Moreover, MMP2 and MMP9 were expressed in (71.8% and 64.1%) in breast cancer tissues compared to (28.6% and 23.8%, respectively) in benign tumor tissues. OCT3/4, ALDH-1, CD44 and ABCG2 were significantly related with cancer types (P=0.001, 0.003, 0.001 and 0.01), cancer grades (P=0.003, 0.004, 0.01 and 0.01) and with lymph node metastasis (P=0.005, 0.05, 0.001 and 0.0001, respectively). No significant correlation between the expression levels of these markers and other clinicopathological data. Moreover, MMP2 and MMP9 are related with tumor stages (P=0.03 and 0.003), Tumor types (0.004 and 0.05), tumors grades (0.04 and 0.01) and with lymph node metastasis (0.009 and 0.04, respectively). In conclusion, the expression levels of OCT3/4, ALDH-1, CD44 and ABCG2 were increased in Iraqi women with stage II-III breast cancer. The high expression levels of these markers were associated with patient's clinicopathological data and may play important roles in cancer progression, speared and metastasis. Moreover, MMP2 and MMP9 could be used as worthy markers in diagnosis and grading of breast cancer. MMP2 expression in nuclear of breast cancer tissues may play important roles in breast cancer progression and metastasis.