Abstract Introduction/Objective Accurate detection of high-grade urothelial carcinoma (HGUC) relies on multiple diagnostic modalities, including UroVysion FISH and urine cytology; however, discordant results between these diagnostic tools can present a challenge. We present this study, scrutinizing the discordant results between UroVysion FISH and urine cytology to explore the potential factors that could contribute to discrepancies. Methods/Case Report A cohort of 118 patients, who underwent both UroVysion FISH and urine cytology testing for evaluation of HGUC, was selected from our cytopathology archives. Results of both the modalities were compared, and a retrospective review of original slides was done by experienced cytopathologists. Results (if a Case Study enter NA) Among the 118 cases, Urovysion FISH yielded positive results in 14 cases and negative in 104. In contrast, urine cytology reported 1 case as positive, 102 as negative, 10 as atypical (8 atypical and 2 rare atypical), and 5 as suspicious. Discordant findings were observed in 20 cases, accounting for 17% of the cases. After retrospective review of original slides, few cases were reclassified. 2 cases as atypical (initially labeled as negative), 2 cases as negative (initially labeled as atypical), 3 cases as positive (initially labeled as atypical/suspicious), 3 cases as suspicious (initially labeled as negative/atypical). Conclusion This reclassification highlights complexity of cytological interpretation, including the challenges of distinguishing between benign cellular alterations, reactive changes, ambiguous findings, suspicious features and malignant cytological changes. Integrating molecular and morphological assessment is essential for evaluation of urothelial carcinoma. Discrepancy between the two is an area which is open to study and can be related to differences in sensitivity and specificity of the testing modalities, sampling methods, variation in interpretation, limitations of testing modality and varying tumor characteristics. Review of clinical history, imaging studies, cystoscopy, and repeat testing may be considered in such cases for diagnostic accuracy.