It is well established that benign proliferative lesions and atypical hyperplasia increase the risk of breast cancer, which can develop in either breast. At present, there is no radiological, pathological, or molecular marker capable of distinguishing which proliferative or atypical lesions will progress to carcinoma. EZH2, a protein involved in stem cell renewal and carcinogenesis is upregulated in the morphologically normal breast epithelium from BRCA1 mutation carriers. Here, we tested the hypothesis that EZH2 expression alone or in combination with the breast stem cell marker aldehyde dehydrogenase-1 (ALDH-1) may identify benign breast biopsies that progress to breast cancer in the future. Benign breast biopsy samples obtained from 59 women who subsequently developed (study group, n=29) or who did not develop (control group, n=30) breast cancer in the same time period were subjected to immunohistochemical analyses of EZH2 and ALDH-1 proteins. When present, EZH2 was expressed in the nuclei of benign epithelial cells, whereas ALDH-1 was expressed in the cytoplasm of epithelial cells and/or in the stroma. EZH2, epithelial ALDH-1, and expanded stromal ALDH-1-positive cells were present in 95, 43, and 69%, respectively, of study group biopsies, compared with 16, 13, and 37%, respectively, of control biopsies (P <0.05 for all). The mean percentage of EZH2-positive cells was higher in the study group than in the control group (34 and 6%, respectively). EZH2 expression was associated with breast cancer development (P=8.2 × 10(-6)) and with younger age at cancer diagnosis (P=0.0086). Both stromal and epithelial ALDH-1 were associated with development of breast cancer (P=0.001 and P=0.049, respectively). Our study provides first evidence that EZH2 and epithelial and stromal ALDH-1 detection in benign breast biopsies may predict increased risk for breast cancer, with implications for breast cancer prevention.