Background Multicenter laboratory may apply both automated flow cytometer and microscopy for urinalysis. Automated flow cytometer such as Sysmex UF-1000i evaluates particles with native urine without centrifugation and reports as "counts per mu L." Microscopic examination recommended as the reference method for urine sediment analysis reports results as "counts per HPF (or mu L)." Moreover, some results from flow cytometer are needed to be checked visually under microscopy. Therefore, it is worth to establish the consistency of the results from these two methods. Methods Urine specimens from 412 patients were examined with Sysmex UF-1000i and manual microscopy using FAST-READ disposable counting chambers. White blood cell (WBC) and red blood cell (RBC) counting results from UF-1000i after transferred with the converting factor (0.297) we estimated were compared with that from microscopic examination. Method comparison was performed using Passing-Bablok analysis. Results After transferred with the converting factor (0.297), cell counting results from UF-1000i showed a good correlation with that derived by the reference method (R-2 was 0.868 for RBCs (P < 0.001), 0.882 for WBCs (P < 0.001)). Passing-Bablok analysis showed no systematic difference (intercept estimate, -1 [95%CI, -7 to 3] and slightly proportional (slope estimate, 1.2 [95%CI, 1.0 to 1.7]) bias between concentrations of cells measured by manual microscopy and Sysmex UF-1000i using the converting factor. Conclusion The converting factor (0.297) helps to transfer "counts per mu L (non-centrifugal urine)" to "counts per mu L (equal to centrifugal urine)," and to keep the urine particle analysis results of Sysmex UF-1000i consistent with the results from the reference method.