CD44+/CD24−/low tumor cells or aldehyde dehydrogenase 1 (ALDH1) positive tumor cells are considered cancer stem cells (CSCs) that possess the properties of self-renewal and tumorigenicity. However, their clinical value and significance in breast cancer remain controversial. A meta-analysis based on published studies was performed with the aim of obtaining an accurate evaluation of the association between the presence of CSCs in clinical samples and clinical outcome. A total of 12 eligible studies with 898 cases and 1,853 controls were included. CSC positive breast cancers, in particular those positive for ALDH1, were significantly associated with high histological grade, estrogen receptor (ER) negativity, progesterone receptor (PR) negativity, and human epidermal growth factor receptor type 2 (HER2) positivity. However, the presence of cancer stem cells was not associated with tumor size or nodal status. ALDH1 positive (RR = 2.83, 95% CI: 2.16–3.67, P < 0.001) and CD44+/CD24−/low tumor cells (RR = 2.32, 95% CI: 1.51–3.60, P < 0.001) were significantly associated with poor overall survival (OS). The stem cell markers are prognostic factors in breast cancer. Larger clinical studies are required to further evaluate the role of these markers in clinical practice.