Currently, prostate cancer is the second leading cause of death from cancer in North America, the most frequent malignancy in men from all ethnicities, surpassing lung cancer. Prostate tumors are highly heterogeneous and there are many studies evaluating the molecular profile or ‘fingerprint’ of prostate cancer. Conventional analysis reviews the protein expression of key markers via serum analysis and immunohistochemistry (IHC) of the biopsy. In this presentation we will review how RNA in situ hybridization (ISH) analysis of prostate cancer can unravel the molecular heterogeneity of the tumor, identify molecular subsets and detect key fusions and mutations of the RNA. We will also present a comparison of IHC and ISH technology and the combination of dual color IHC and dual color ISH can be used to enhance simultaneous evaluation of DNA, RNA and protein, revealing the molecular profile of prostate cancer.