Background/Aims: Liquid based cytology (LBC) was developed as a replacement for cytocentrifugation in the treatment of cell suspensions. Because accurate data comparing the quality and total cost of modern cytocentrifugation methods versus LBC in non-gynaecological samples are not available, this study was designed to investigate these issues. Methods: The study comprised 224 urine samples treated with the Thermo Shandon Cytospin® 4 using reusable TPX® chambers, disposable Cytofunnels® for samples up to 0.5 ml, and disposable Megafunnels® for samples up to 6 ml. Each method was compared with the Cytyc Thinprep® processing of a paired sample. Quality was assessed by scoring cellularity, fixation, red blood cells, leucocytes, abnormalities of urothelial cells, and suitability for molecular studies. Wage costs, investment, and consumables allowed a “total cost” to be calculated on the basis of 200 specimens/month. Total cost and quality combined were used to calculate an index of total quality (ITQ). Results: Cytocentrifugation with disposable chambers resulted in a global quality superior to that of Cytyc Thinprep LBC. Preparation and screening times were 2.25 and 1.33–2 times greater when using LBC compared with cytocentrifugation. The total cost each month reached 1960.23 $ to 2833.43 $ for cytocentrifugation methods and 5464.95 $ for Cytyc Thinprep LBC (92.8–178.8% increased cost). ITQ of cytocentrifugation with disposable chambers surpassed that of Cytyc Thinprep LBC (37.25/32.08 and 9.98, respectively). Conclusion: Cytyc Thinprep LBC and cytocentrifugation are both appropriate methods for cytology based molecular studies, but cytocentrifugation remains the quality standard for current treatment of urinary samples because of its lower cost.