The selection of a systemic breast cancer therapy is based on the expression pattern of immunohistochemical prognostic markers. In our study we sought to determine whether neoadjuvant chemotherapy may alter these expression patterns within the tumors. Our hypothesis was that the expression of the immunohistochemical prognostic markers does not differ between tissue specimens before and after neoadjuvant chemotherapy. We determined the protein expression levels of estrogen receptor, progesterone receptor, Ki67, p53 and HER2/neu in the core biopsy and the resected tumor sample from 25 patients receiving neoadjuvant chemotherapy. As a control group, we analyzed sample pairs from 30 patients who did not receive neoadjuvant chemotherapy. Additionally, we determined the relative HER2/neu gene copy number by FISH and/or real-time PCR. There were no significant differences in the changes in expression patterns from the core biopsy to the treated resected tumor between those who had received neoadjuvant chemotherapy and the control group. We suggest that it is sufficient to analyze the prognostic factors from either the core biopsy prior to chemotherapy or the treated tumor sample instead of investigating both samples. This would markedly reduce the costs.