Introduction: The aim of this study was to compare performance of individual categories between the Johns Hopkins template and the Paris system for reporting urinary cytology. Methods: Medical records of patients with bladder biopsy and relevant cytology slides were obtained from archived material. Slides were reclassified according to Johns Hopkins template and the Paris system. Results were compared to histological diagnoses. Results: BD SurePath preparations from 205 cases with biopsy follow-up (118 benign, 5 dysplasia, 23 low, and 59 malignant urothelial carcinoma [UC]) were reviewed. There were 2 inadequate specimens in each system. According to the Johns Hopkins template, there were 96 (46.8%) no urothelial atypia or malignancy, 37 (18%) atypical urothelial cells of uncertain significance (AUC-US), 21 (10.2%) atypical urothelial cells, cannot exclude high-grade urothelial carcinoma (HGUC), 38 (18.5%) HGUC, and 11 (5.4%) low-grade urothelial carcinoma (LGUC). The Paris system categorized 111 (54.1%) negative for high-grade urothelial carcinoma, 29 (14.1%) atypical urothelial cells (AUCs), 25 (12.2%) suspicious for HGUC (SHGUC), 36 (17.6%) HGUC, and 2 (1%) LGUC. The Johns Hopkins template had a sensitivity of 95.6%, specificity of 73.6%, positive predictive value of 61.5%, negative predictive value of 96.3, with an overall diagnostic accuracy of 79.8%. The Paris System had a sensitivity of 93.6%, specificity of 77.9%, positive predictive value of 65.6%, negative predictive value of 96.5, with an overall diagnostic accuracy of 82.8%. The risk of malignancy (ROM) for atypical category (AUC-US/AUC) in the Johns Hopkins template was 43.2%, while it has been 24.1% for the Paris System. The ROM for suspicious category was 47.6% and 68.0%, respectively. There were statistically significant differences between negative and atypical, suspicious, and HGUC categories in each system (p < 0.0001). Conclusions: Discrete negative or benign urine cytology had the same sensitivity and specificity between two systems. Although atypical category was associated with a higher ROM with the Hopkins template, the ROM for the suspicious category yielded better result with the Paris system.