This study evaluated the relative frequencies of HER-2/neu gene amplification in ductal carcinoma in situ (DCIS)-associated invasive breast cancer and DCIS alone. We examined archival tissue samples of 100 DCIS lesions with an invasive component (cases) and 100 without an invasive component (controls), with cases and controls matched by pathologic nuclear grade. HER-2/neu gene amplification was determined by fluorescence in situ hybridization. We compared HER-2/neu gene amplification in DCIS lesions only, irrespective of the presence or absence of an invasive component. HER-2/neu gene amplification occurred significantly less frequently in the cases (26%) than in the controls (40%), with an odds ratio of 0.35 (95% confidence interval, 0.17-0.72; P < 0.004) after adjustment for pathologic and quantitative-image-analyzed morphometric nuclear grade. The HER-2/neu gene also was amplified more frequently in higher- than in lower-grade DCIS alone (56% versus 19%, respectively; P < 0.0001) or in higher- than in lower-grade DCIS with invasive cancer (44% versus 2%, respectively; P < 0.00001). Future studies should examine the potential roles of HER-2/neu and other biomarkers (e.g., p21 and Rb) as markers of the risk of DCIS patients for invasive breast cancer and as molecular targets of chemoprevention in breast intraepithelial neoplasia.