At present there are no clinically useful markers available for identifying bladder cancer patients with a high risk of disease recurrence or progression. Thus, identification and tailor-suited treatment, for example radical cystectomy and adjuvant therapy, of patients with a poor prognosis is not possible using current methods. The completion of the Human Genome Project and the simultaneous advances in microarray technology have paved the way for performing systematic, full genome screens for prognostic and diagnostic molecular cancer markers. Furthermore, utilization of microarray technology for identifying clinically relevant subclasses of cancer patients and for discovering new potential drug targets seems promising. This article summarizes some of the clinical aspects of bladder cancer and reviews the potential of using tumor expression profiling for the identification of new molecular cancer markers and drug targets, and for generating disease classifiers and outcome predictors using several key gene markers.