Centrifuged and filtered urine is often used to evaluate in vitro the crystallization processes of calcium oxalate (CaOx), but even such simple manipulations can alter the composition of the urine, as regards its protein and lipid concentrations. In urine samples taken from 17 normal male adults, we evaluated CaOx crystallization by simultaneously using three different types of urine: untreated (U), centrifuged at 2000 rpm (800 g) and filtered at 0.22 microm (CF), and centrifuged-filtered and ultrafiltered at 10 000 Da (CFU). The addition of 1.2 mmol/l of oxalate to each type of urine produced notably different results. The total amount of CaOx crystals (expressed as calcium oxalate dihydrate crystals (COD) + oxalate monohydrate crystals (COM) area/total area x 100) was on average 13.2% in U urine, 70.7% in CF urine and 11.1% in CFU urine (CF > U and CFU, U = CFU); the relative prevalence of COD and COM (expressed as COD area/COM area) was on average 71.4 in U urine, 0.0026 in CF urine and 5.5 in CFU urine (U > CF and CFU, CFU > CF); the diameter of COD (expressed in microns) was on average 15.2 in U urine, 3.7 in CF urine and 24.3 in CFU urine (CFU > U and CF, U > CF); the diameter of COM (expressed in microns) was on average 5.2 in U urine, 2.6 in CF urine and 8.9 in CFU urine (CFU > U and CF, U > CF); the total amount of CaOx aggregates (expressed as CaOxAgg area/total area x 100) was on average 8.5% in U urine, 22.1% in CF urine and 2.9% in CFU urine (CF > U and CFU, U > CF). We conclude that CaOx crystallization processes in manipulated urine are extremely different, probably due to changes in macromolecular compounds.