BACKGROUND The aim of this study was to evaluate the potential use of the UroVysion® fluorescent in situ hybridization test (U-FISH) to stratify the risk of urothelial carcinoma (UC) in patients with a diagnosis of "atypical urothelial cells" (AUC) in urinary tract cytology (UTCy). METHODS Using a histologic diagnosis of UC and respectively of high grade UC (HGUC) within 12 months of the index UTCy as a reference standard, we determined the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy of U-FISH for patients with AUC diagnosed 2008 to 2014. RESULTS Of the 377 patients with AUC, 62 (16.45%) were diagnosed with UC (29 low grade UC and 33 HGUC) within 12 months. U-FISH were uninformative in 45 (11.94%), positive in 63 (16.71%) and negative in 269 (71.35%). UC was diagnosed more frequently in patients with positive than in those with negative U- FISH results (31/63, 49.21% vs. 25/269, 9.29%, P