HER-2/neu status is critical for the therapy for breast carcinoma. Fluorescent in situ hybridization for gene amplification and immunohistochemical stains for protein expression are widely used methods to detect HER-2/neu status. Multiple studies have shown fluorescent in situ hybridization and immunohistochemical stain results to have high concordance rates. To our knowledge, a comparison between fluorescent in situ hybridization results for core needle biopsy and the subsequent excisional biopsy specimens has not yet been studied. We retrospectively evaluated the fluorescence in situ hybridization and immunohistochemical results in both the breast core needle and the excisional biopsy of 125 patients with invasive breast carcinoma from 2002 to 2005. There was complete concordance with respect to both immunohistochemical and fluorescence in situ hybridization results for core needle biopsy and excisional biopsy specimens in 87% of the patients evaluated. Comparison of fluorescent in situ hybridization results of the 129 core needle biopsies to the 131 excisional biopsies of all 125 patients showed a concordance rate of 92%. The immunohistochemical stain results of the same core needle and excisional biopsies showed a concordance rate of 98%. Comparison of the immunohistochemical stain results with the fluorescent in situ hybridization results for all 260 cases examined showed 95% concordance. On the basis of our study, we observed that repeating HER-2/neu testing by immunohistochemical stain and/or fluorescent in situ hybridization methods on excisional biopsy is not unreasonable, in particular in cases of intratumoral heterogeneity, indeterminate/borderline HER-2/neu results and after neoadjuvant chemotherapy.