The question is raised whether the new theories about initiation and progression of urothelial carcinoma gained by molecular techniques show effects on the classification and histopathological diagnosis. As fundamental new concepts are considered: two pathways of tumor progression, clonality of synchronous and metachronous tumors, tumor-analogous molecular findings in flat lesions, and stromal invasion as dominant principle of molecular tumor classification.The dual pathogenesis of molecular pathology is reflected by the WHO 2004 classification by the differentiation into low and high grade malignancy, but diluted by the use of PUNLMP (papillary urothelial neoplasia of low malignant potential). The new concept of frequent oligoclonality should induce investigations about the mechanism of propagation of these migrating or metastasizing cells and whether they possess stem cell characteristics. The role of flat urothelial lesions must be revised from a molecular pathological view point, but the histological diagnosis does not gain profit till now. The expression signatures of stromal invasive tumors compared with non-invasive ones points to the major importance of an exact histopathological diagnosis in this area.