BACKGROUND: The UF-100 flow cytometer (Sysmex Co., Japan) and the Iris iQ200 (Iris Diagnostics, USA) are widely used for routine urinalysis in Korea. We compared the diagnostic accuracy of these two automated systems based on the microscopic finding, and evaluated the clinical performance of the automated systems. METHODS: A total of 323 fresh urine samples were selected and analyzed by conventional microscopy and the automation systems, the UF-100 and the iQ200. Quantification for RBCs, WBCs, and bacteria were also evaluated using both automated systems. RESULTS: For 158 of urine sample classified as normal urines, the agreement rate for the UF-100 and the iQ200 was 84.8% (N=134) and 89.9% (N=142), respectively. For 165 of urine samples classified as abnormal urines, the agreement rate for the UF-100 and the iQ200 was 90.9% (N=150) and 81.8% (N=135), respectively. The UF-100 showed a good linearity in the quantitative measurements of RBCs and WBCs. For both systems, false-negative value for WBCs and bacteria were about 30% in abnormal urines. Both systems showed inaccurate results for pathologic casts and bacteria. CONCLUSIONS: We compared the microscopic finding and the primary results of automated systems without user reclassification, and the agreement rate was about 85%. The agreement rate will be improved by deliberating "Review" comments of the instruments.