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Introduction: Automated urinalysis systems are valuable tools in clinical laboratories, especially those with a high work load. The objective of this study was to compare the analytical performance of Sysmex UN series urine analyser, which may become a new one in our laboratory, with the Cobas 6500 automated urine analyser, which is used in our laboratory for a long time. For comparisons, manual microscopical examination was accepted as reference method. Materials and methods: A total of 470 urine samples were tested in the two automated urinalysis systems, and urine sediment testing with manual microscopy was applied to a 100 pathological samples of the total 470. The diagnostic performance of the two automated urine analysers was compared with each other and manual microscopy. Results: Differences were determined between automated and manual microscopy in some pathological samples. The resultant regression equations were as follows. Comparison of Cobas U701 with Sysmex UF-5000: y = - 0.57 (- 0.85 to - 0.29) + 0.95 (0.92 to 0.99) x for RBC, and y = - 0.11 (- 0.54 to 0.29) + 0.89 (0.84 to 0.98) x for WBC; comparison of Cobas U701 with manual microscopy: y = - 0.45 (- 0.85 to 0.21) + 1.00 (0.92 to 1.07) x for WBC; and comparison of Sysmex UF-5000 with manual microscopy: y = - 0.74 (- 1.09 to - 0.57) + 0.87 (0.85 to 0.91) x for WBC. Conclusions: We can conclude that the new Sysmex UN series urine analyser can be safely used in our laboratory. Although the results showed good to moderate concordance, the microscopy results of the automated platforms should be confirmed by manual microscopy, particularly in pathological samples.