Lipoprotein lipase (LPL) plays a key role in lipid metabolism by hydrolyzing triglycerides in circulating lipoproteins. Low LPL activity has been linked to coronary artery disease (CAD), but the factors influencing LPL expression are not completely understood. Peroxisome proliferator--activated receptor (PPAR)-gamma is a nuclear receptor regulating lipid and glucose metabolism, and a PPAR-responsive element is present in the LPL promoter. We determined the Pro12Ala polymorphism in the PPAR-gamma2 gene in 194 male CAD patients because this allele is associated with decreased PPAR activity and reduced LPL promoter activity in vitro. Presence of 12Ala was associated with 20% lower LPL activity in postheparin plasma (141 +/- 58 vs. 177 +/- 77 nmol.ml(-1).min(-1), P < 0.005). Remarkably, the influence of 12Ala on LPL was greater than that of the frequent polymorphisms (HindIII +9%, PvuII +/- 0%, 447stop +12%) in the LPL gene itself. To confirm these results in a different group of patients, we analyzed 100 diabetic patients in whom the 12Ala allele was also associated with lower LPL activity (12Ala: 132 +/- 88 vs. 190 +/- 129 nmol.ml(-1).min(-1), P < 0.05). Our data demonstrate that the Pro12Ala substitution in PPAR-gamma2 is associated with lower LPL activity in vivo and provides a new target for the analysis of genetic influences on LPL activity and CAD risk.