Urothelial cancer, bladder cancer, is divided in two major subtypes, non-muscle invasive and muscle-invasive, with very distinct biological and clinical properties. Prognosis and treatment are mainly based on pathological criteria. The fact that only 20-25% of high grade low stage tumors are confirmed by review pathology, and that 30% of patients with intermediate stage tumors are upstaged after repeated transurethral resection (TUR), argues that standard pathological methods is unreliable for proper tumor assessment. To address these problems we have constructed a molecular taxonomy of urothelial cancer. This taxonomy is based on a combination of gene expression, epigenetic and genomic changes, and gene mutations analyses. The overall goal is to refine and optimize UC classification into molecular subtypes important for prognosis and treatment.