Peroxisome proliferator-activated receptors gamma2 and alpha are nuclear factors known to be important regulators of lipid and glucose metabolism. Two polymorphisms, namely PPARgamma2 P12A and PPARalpha L162V, were investigated for their individual and interaction effects on glucose and insulin homeostasis. Genotypes were determined in 663 nondiabetic adults participating in the Québec Family Study and who underwent an oral glucose tolerance test (OGTT). The insulin and C-peptide areas under the curve (AUC) following the OGTT were higher in subjects carrying the PPARalpha V162 allele compared to homozygous for the L162 allele. When subjects were grouped according to both polymorphisms, higher levels of insulin and C-peptide during the OGTT were observed for those carrying the PPARalpha V162 allele except when they carry at the same time the PPARgamma2 A12 allele. Thus, the PPARgamma2 A12 allele seems protective against the deleterious effect of the PPARalpha V162 allele. Furthermore, a significant gene-gene interaction was observed for the acute (0-30 min) (p<0.001) and the total (p=0.05) C-peptide AUC following the OGTT. These results provide evidence of a gene-gene interaction in the regulation of plasma glucose-insulin homeostasis, and emphasize that these interactions need to be taken into account when dissecting the genetic etiology of complex disorders.