Peroxisome proliferator-activated receptors (PPARs) are nuclear hormone receptors mediating ligand-dependent transactivation. Among the 3 isoforms, PPAR-α is involved in lipid metabolism in the liver, while PPAR-γ(-γ1 and -γ2) is involved in adipocyte differentiation. Recently, PPARs have been suggested to be involved in renal electrolyte metabolism as well as atherosclerosis. PPAR-α is known to regulate cytochrome P450 gene expression, and may possibly affect sodium retention in the kidney. Moreover, PPAR-γ is involved in the transcription regulation of blood pressure regulatory genes, including thromboxane and angiotensin II type 1 receptors. In the kidney, although expression of PPARs has been reported, detailed immunohistochemical analyses have not been performed. We here generated isoform-specific anti-PPAR antibodies to localize their proteins in the kidney. Anti-PPAR antibodies were raised against synthetic peptides. Their isoform specificity was confirmed by immunoblot analyses, immunoprecipitations, and antibody supershift experiments by electrophoretic mobility shift assay. We therefore studied the protein expression of PPARs in the kidney of adult Sprague-Dawley rats using these antibodies. Immunoblot analyses demonstrated protein expression of PPAR-α and -γ1, but not of -γ2, in the kidney nuclear extracts. Immunohistochemical analyses demonstrated that both PPAR-α and -γ1 proteins were widely expressed in the nuclei of mesangial and epithelial cells in glomeruli, proximal and distal tubules, the loop of Henle, medullary collecting ducts, and intima/media of renal vasculatures. PPAR-α and -γ1 proteins are thus widely expressed along the nephron segments, and may affect gene expression at these segments. Further studies will be needed to identify additional target genes for PPARs along the nephron segments. (Hypertens Res 2004; 27: 417-425)