Multiprobe fluorescence in situ hybridization (FISH) still remains the gold standard for clarifying inconclusive atypia in urinary cytology in daily routine practice. The Paris Classification System (The Paris System, TPS) provides an important basis for the specific indication of FISH and emphasizes the importance of morphological correlation for an integrative approach to diagnosis. Next-generation sequencing technology in urinary specimens, which is highly sensitive for simultaneous detection of multiple genetic alterations, is also likely to play a diagnostic role in the near future.