Reliable detection of poorly differentiated urothelial carcinoma and the detection of carcinoma in situ, which is often invisible by cystoscopy, are the undisputed strength of urinary cytology. In contrast, well-differentiated urothelial tumors are often missed by cytology. We suggest the following classification: negative, questionable, suspicious, and positive. Due to the complex clinico-pathological associations, the classification should always be accompanied by an appropriate commentary. The WHO 2004 classification separates the clinically less important low-grade tumors from the clinically relevant high-grade tumors, usually classified as "positive" by cytology. A cytological diagnosis of low-grade tumors by cytology is of minor clinical importance. Most urothelial neoplasias are characterized by chromosomal aberrations. This makes multi-target fluorescence in situ hybridization (FISH) assay suitable for the clarification of non-definitive cytology. In contrast, positive cytology does not need further confirmation by FISH analysis. Standardized diagnosis and the possibility for supplementary analyses increase the diagnostic value of urinary cytology.