The prognostic and therapeutic implications of estrogen receptor (ER) status in breast cancer are well known. Whether ER status plays a role in benign breast lesions and the progression to malignancy has not been proven. Enlarged lobular units with columnar alteration (ELUCA), also known as unfolded lobular units, have been associated with mild elevations in subsequent breast cancer risk. We examined the association of ERalpha expression in ELUCA with invasive breast cancer risk. A nested case-control study was performed of women with ELUCA who had undergone benign breast surgery. Eighty-two women who developed invasive breast cancer on follow-up were matched by age and year of biopsy with 166 women who did not develop invasive breast cancer. Entry biopsies were stained for ERalpha (clone 6F11) without knowledge of subsequent cancer outcome. ELUCA lesions were scored as positive if greater than 10% of epithelial nuclei stained with ERalpha and at least one ELUCA contained >50% of cells staining for ERalpha. Relative risks of breast cancer were estimated by odds ratios derived from conditional logistic regression analyses. Thirty-nine percent of cases and 56% of controls had positive ERalpha staining in ELUCA. The relative risk of invasive breast cancer in women with ERalpha-negative ELUCA was 1.85 times that of women with ERalpha-positive lesions (95% confidence interval, 1.0-3.4, P=0.04). The presence of ERalpha staining in women with ELUCA is associated with a lower risk of developing subsequent invasive carcinoma. These findings have implications for risk assessment in benign breast biopsies and are of particular interest given the controversy currently surrounding hormone replacement therapy.