HER2 and TOP2A genes, located on 17q, can be coamplified in cancer. Overexpression of both genes has been reported in high-grade, androgen-resistant prostate cancer. Both genes have not been compared in a single prostate cancer study and the frequency of TOP2A amplifications in prostate cancer is unknown. Using tissue microarrays, we did immunohistochemistry and fluorescence in situ hybridization for HER2 and TOP2A in 100 prostate cancers (41 localized and 59 advanced) and 42 cases of benign prostatic hyperplasia (BPH). Amplification was defined as a target/centromere signal ratio of > or =1.5. HER2 immunohistochemistry was scored from 0 to 3+. Percentage nuclei staining for topoisomerase IIalpha (topoIIalpha) was recorded; overexpression was defined as > or =5% cells staining. Eighteen (31%) advanced prostate cancers showed topoIIalpha overexpression; 12 (26%) showed TOP2A low-level amplification; 9 (16%) expressed HER2; and 6 (13%) showed HER2 low-level amplification. No high-level amplification of either gene (target/centromere signal ratio of > or =3.0) was detected. TOP2A coexpression and coamplification were seen in 75% and 66% of HER2-positive cases, respectively. Localized prostate cancer or BPH showed no gene amplification or topoIIalpha overexpression. Gene amplification or overexpression correlated with high stage and Gleason score. The presence of TOP2A amplification in advanced cancer was associated with androgen resistance and decreased survival by multivariate analysis. This is the first study to document low-level TOP2A amplification in prostate cancer and an association with reduced survival. TOP2A amplification may occur with or without HER2 duplication and is often associated with topoIIalpha expression. Therapies directed against topoIIalpha (and HER2) in such patients may improve survival.