Studies employing whole genome and exome sequencing have revealed two remarkable features of prostate cancer (PCa)—the overall low mutation rates, and high rates of genomic rearrangements resulting in recurrent gene fusions. Genomic rearrangements involving the ETS transcription factor family genes are early driver events in PCa. These rearrangements typically involve the fusion of androgen-regulated transcriptionally active genes with the ETS genes (ERG, ETV1, ETV4 and ETV5), resulting in over-expression of fusion genes. The most prevalent ETS gene rearrangement, which is observed in >50% of PCa, involves the fusion of the androgen receptor (AR) target gene, TMPRSS2, with the ERG proto-oncogene, resulting in the formation of the TMPRSS2-ERG gene fusion. In this chapter, we consider the multitude of factors that influence the formation of recurrent genomic rearrangements in PCa. Understanding the mechanistic basis of gene fusion formation will shed light on unique features of PCa etiology and should impact several aspects of clinical disease management, ranging from prevention and early diagnosis to therapeutic targeting.