Breast cancer stem cells are thought to be associated with metastasis and poor prognosis, but their clinical importance remains poorly understood. The aim of this study was to investigate whether certain phenotypes of breast cancer stem cells were clinically important factors regarding metastasis. Patients with primary breast cancer (n=121) were included in this study. Breast cancer stem cells were identified by immunohistochemical staining of CD44, CD24, and aldehyde dehydrogenase 1 (ALDH1) in tumor tissues from primary and recurrent or metastatic lesions. CD44+/CD24- cells and ALDH1+ cells were considered breast cancer stem cells. Sixty-five patients had metastatic or recurrent tumors. ALDH1+ tumors were significantly associated with a high rate of metastasis or recurrence (63.1%; P=0.026). Although there was no significant association between the proportion of CD44+/CD24- tumor cells and metastasis rates, a high proportion of CD44+/CD24- tumor cells was a risk factor for metastasis or recurrence (P=0.035). Changes in the proportion of CD44+/CD24- or ALDH1+ tumor cells between primary lesions and recurrent lesions were studied in 27 patients. The proportion of ALDH1+ tumor cells increased significantly (P=0.019) after recurrence, but the proportion of CD44+/CD24- tumor cells did not. Our findings suggest that ALDH1+ and CD44+/CD24- breast cancer stem cells play significant roles in metastasis. The rate of ALDH1+ cells appears to be a better predictive marker of breast cancer metastasis than the CD44+/CD24- phenotype.