Despite the physiological and evolutionary significance of lipid metabolism in amniotes, the molecular mechanisms involved have been unclear in reptiles. To elucidate this, we investigated peroxisome proliferators-activated receptors (PPARs) in the leopard gecko (Eublepharis macularius). PPARs belong to a nuclear hormone-receptor family mainly involved in lipid metabolism. Although PPARs have been widely studied in mammals, little information about them is yet available from reptiles. We identified in the leopard gecko partial cDNA sequences of PPARα and β, and full sequences of two isoforms of PPARγ. This is the first report of reptilian PPARγ mRNA isoforms. We also evaluated the organ distribution of expression of these genes by using RT-PCR and competitive PCR. The expression level of PPARα mRNA was highest in the large intestine, and moderate in the liver and kidney. The expression level of PPARβ mRNA was highest in the kidney and large intestine, and moderate in the liver. Similarly to the expression of human PPARγ isoforms, PPARγa was expressed ubiquitously, whereas the expression of PPARγb was restricted. The highest levels of their expression, however, were observed in the large intestine, rather than in the adipose tissue as in mammals. Taken together, these results showed that the profile of PPARβ mRNA expression in the leopard gecko is similar to that in mammals, and that those of PPAR α and γ are species specific. This may reflect adaptation to annual changes in lipid storage due to seasonal food availability.