The genetic basis of 50–60% of prostate cancer is attributable to rearrangements in ETS (ERG, ETV1, ETV4, and ETV5), BRAF and RAF1 genes and overexpression of SPINK1. The development and validation of reliable detection methods are warranted to classify various molecular subtypes of prostate cancer for diagnostic and prognostic purposes. ETS gene rearrangements are typically detected by fluorescence in situ hybridization (FISH) and reverse transcription PCR methods. Recently, monoclonal antibodies against ERG have been developed that detect the truncated ERG protein in immunohistochemical assays where staining levels are strongly correlated with ERG rearrangement status by FISH. However, specific antibodies for ETV1, ETV4 and ETV5 are unavailable, challenging their clinical use. We developed a novel RNA in situ hybridization based assay for the in situ detection of ETV1, ETV4, and ETV5 in formalin fixed paraffin embedded tissues from prostate needle biopsies, prostatectomy, and metastatic prostate cancer specimens using RNA probes. Further, with combined RNA in situ hybridization and immunohistochemistry we identified a rare subset of prostate cancer with dual ETS gene rearrangements in collisions of independent tumor foci. The high specificity and sensitivity of RNA in situ hybridization provides an alternate method enabling bright field in situ detection of ETS gene aberrations in routine clinically available prostate cancer specimens.