Background: Recent studies have suggested a link between levels of TOP2A expression, carcinogenesis and response to anthracycline based chemotherapy. It has been postulated that this relationship may be due the co-amplification of the HER2 and TOP2A genes. Some investigators have suggested that evaluation of TOP2A protein level may be more useful than gene alterations. Methods: In this study, the gene copy number using in-situ hybridization and protein expression using immunohistochemistry of both TOP2A and HER2 were evaluated in four independent series of breast cancers (BC): a) 240 locally advanced primary BC treated with anthracycline-based combination with or without taxane followed by surgery; pathological complete response (pCR) was used as the study end point, b) 245 BC in which all patients were primarily treated with surgery followed by anthracycline-based chemotherapy, c) 145 primary BC overexpressing HER-2 treated with surgery followed by trastuzumab and d) 2000 consecutive cases of primary BC in which adjuvant CMF and/or Tamoxifen therapies were prescribed. The association between gene and protein alteration of TOP2A and clinicopathological outcomes was determined. Results: In patients who received CMF chemotherapy and/or Tamoxifen, TOP2A protein overexpression was associated with HER2 amplification/overexpression (p=0.02), p53 mutation (p=0.03), a high mitotic index (p=0.01) and high proliferation index (p=0.04), but did not show any association with outcome. In patients who received anthracycline based treatment TOP2A gene amplification predicted a better disease free survival (p=0.026). In the anthracycline-based neoadjuvant chemotherapy series, the pCR rate was 31/132 (24%) in tumours expressing high levels of Topo2A, compared to 3/49 (6%) in tumours expressing low levels of Topo2A. (p=0.008). In multivariate analysis, TOP2A expression was an independent predictor for pCR (p<0.01). Conclusions: Alterations in TOP2A protein are an independent predictor of response to anthracycline based treatment in both the adjuvant and neoadjuvant setting. TOP2A overexpression could be a marker of high proliferative tumours.