Extensive lists of molecular biomarkers are currently evaluated as potential targets for directed cancer therapies. We reviewed three potential candidate biomarkers to play a role in the near future as molecular theranostics for urologic malignancies. Carbonic anhydrase type IX is a surrogate marker of hypoxia highly expressed in cancer cells. Their expression and clinical significance in kidney and urothelial bladder cancer are discussed as well as the main therapeutic approaches that are currently under evaluation. For prostate cancer, available evidence on the use of prostate-specific membrane antigen and neuropeptide receptors radiolabeled analog and the undergoing clinical studies are also analyzed and discussed at different stages of prostate cancer.