We correlated quantitative results obtained in 40 invasive breast cancer cases for HER-2 gene amplification by fluorescence in situ hybridization with protein expression by immunohistochemical studies with computer-assisted image analysis. Fluorescence in situ hybridization (FISH) results were quantified as the mean number of fluorescent signals per nucleus, and immunohistochemical slides were read by semiquantitatively assessing membranous immunostaining intensity in tumor cells vs nonneoplastic breast tissue or quantitatively evaluated by image analysis. We found high correlation between immunohistochemical results by semiquantitative scoring and by image analysis. FISH results correlated with immunohistochemical results moderately when the staining intensity of only tumor cells was assessed and significantly better when the difference in staining intensity between tumor cells and nonneoplastic breast tissue was assessed. The correlation with FISH results was further improved when immunohistochemical study was combined with heat-induced epitope retrieval (HIER). Although FISH and immunohistochemical studies assess different aspects of the HER-2/neu gene (amplification vs overexpression), we found good correlation between the diagnostic techniques. The correlation was best when immunohistochemical studies were combined with HIER and assessed as the difference between tumor cells and nonneoplastic breast tissue.