Experimental studies showed that paraoxonase-3 (PON3) retards lipoprotein oxidation. Our objective was to describe a new assay to measure serum PON3 concentrations and report their reference values in a population-based study. The influence of PON3 promoter polymorphisms and their relationships with PON1 and lipid profile were also studied. We generated an anti-PON3 antibody by inoculating rabbits with a synthetic peptide specific to mature PON3. This antibody was used to develop an ELISA. The average regression line of standard plots (n = 8) was y = 0.9587 (0.3392) log(10)x + 1.9466 (0.0861) [r(2) = 0.924 (0.0131); P < 0.001]. There was no cross reaction with PON1. Detection limit was 0.24 mg/l. Imprecision was ≤ 13.2%. Reference interval (n = 356) was 1.00-2.47 mg/l. PON3 was observed in HDL particles containing apolipoprotein (apo)A-I and PON1, but not apoA-II or apoE. Serum PON3 concentrations showed a moderate influence (about 10% variation) by PON3 promoter polymorphisms. Our study describes for the first time a method to measure serum PON3 concentrations. This method offers new opportunities in the investigation of the properties and role of PON3 in cardiovascular disease, with possible implications in clinical practice.