A significant proportion of breast cancers with HER2 amplification show simultaneous amplification or deletion of Topo 2. Amplification of Topo 2 may lead to the overexpression of the Topo 2 protein and ultimately to hypersensitivity to Topo 2 inhibitors. HER2 and Topo 2 gene status in breast cancer patients has been determined in several studies using immunohistochemistry, florescence in situ hybridisation (FISH) and multiplex ligation-dependent probe amplification (MLPA). Although comparisons of FISH and MLPA have been reported for HER2, it is believed that there are no similar studies for Topo 2. In this study, HER2 and Topo 2 were analysed by MLPA and FISH. There was a high agreement between the two approaches, although MLPA was easier to perform and cheaper than FISH. In conclusion, MLPA is a fast and accurate quantitative method to detect HER2 and Topo 2 amplification, and could be considered a good alternative to FISH.