The value of urinary cytology in the diagnosis of different pathological conditions in renal transplantation is particularly important. Manual microscopic urinalysis is a high-volume procedure that currently requires significant labour. Objective: To automate the sediment evaluation and to make this more accurate using the Iris Diagnostics Automated Urine Microscopy Analyzer (iQ200). Our goal was to compare the manual and automated microscopic data to apply iQ200 in renal function monitoring. Method: The iQ200 uses digital imaging and Auto Analyte Recognition software to classify urine constituents into 12 analyte categories and quantitatively report. Results: We determined cut-off values of urine particles in every category, which correlated well with manual microscopic results. The iQ200 was more sensitive for pathological casts than manual microscopic analysis. iQ200 helped the operator to differentiate between isomorphic and dismorphic erythrocytes and between lymphocytes and granulocytes, too. Every pathological constituent could be recognized, which is very important for early recognition of renal impairment, graft rejection and urinary tract infection. Conclusions: The iQ200 system automatically classifies 12 particles, significantly reducing the need for additional sample preparation, manual microscopic review achieving a high degree of standardization in urinalysis.