Background Urine cytology has been used for screening of bladder cancer but has been limited by its low sensitivity. UroVysion is a FISH assay that detects common chromosome abnormalities in bladder cancers. The present study evaluates the effectiveness of UroVysion and urine cytology in detecting urothelial cell carcinoma (UCC) in same urine sample. Methods 1,835 cases with the following criteria were selected: valid results of both UroVysion and cytology from same urine sample; histological and/or cystoscopic follow up within 4 months of the original tests, or at least 3 year clinical follow up information. The results of the UroVysion and cytology were correlated with clinical outcome that was derived from combination of histological, cystoscopic and clinical follow up information. Results Of 1,835 cases, 1,045 cases were for surveillance of recurrent UCC, 790 cases were for hematuria. Overall sensitivity, specificity, PPV and NPV in detecting UCC were 61.9%, 89.7%, 53.9% and 92.4%, respectively for UroVysion, and 29.1%, 96.9%, 64.4% and 87.5%, respectively for cytology. The performance of both UroVysion and cytology was generally better in the surveillance population and in samples with high grade UCC. In 95 of 296 cases with atypical cytology that were proven to have UCC, 61 cases, mostly high grade UCC, were positive for UroVysion. Conclusions UroVysion was more sensitive than cytology in detecting UCC, but produced more false positive result. Our data suggest that the use of UroVysion as a reflex test following an equivocal cytological diagnosis may play an effective role for UCC detection.