Molecular biology is expected to provide new tools and approaches to assess the prognosis of patients with bladder cancer, by providing information on the risks of tumor recurrence and progression from superficial bladder cancer to an invasive phenotype. Genetic and epigenetic alterations have been closely associated with bladder carcinogenesis and progression, although most of these are still under investigation in a preclinical setting. This article highlights current findings from molecular studies, and describes their potential application in molecular staging of bladder cancer.