RT-PCR and qPCR are relatively easy to perform. However, to assess multiple potential fusion variants requires multiple sets of primers and probes, and a corresponding large quantity of RNA templates. Moreover, sequencing RT-PCR products is laborious and difficult to adapt in routine clinical laboratories. Here, we describe an exon array-based detection system, combined with a RT-PCR reaction, that accurately determines multiple TMPRSS2:ERG fusion transcripts in specimens with only a minor population of tumor cells. The method adopts several features of the Virochip (25) protocol to establish a specific, sensitive and semi-quantitative assay that is very useful for analyzing highly heterogeneous solid tumors.