Prostate cancer is the most commonly diagnosed neoplasia and the second most frequent cause of cancer specific death in men in the western civilization. The recent discovery and subsequent characterization of recurrent gene rearrangements of ETS genes - most frequently ERG - in the majority of prostate cancers is a milestone in translational prostate cancer research. In this review we summarize the latest findings on the ERG rearrangement in prostate cancer. In particular, we focused on the relevance of the ERG rearrangement as a marker to elucidate the heterogeneity of prostate cancer, a finding which until recently has been difficult to study. Furthermore, since prostate cancer is a multifocal disease in the majority of cases and it is still poorly understood which tumor focus is responsible for metastasis, we explicate the application of the ERG rearrangement as a prostate cancer specific clonal expansion marker.