Light and electron microscopic localization of L-alpha-hydroxyacid oxidase (L-HOX) in rat kidney was studied by means of immunocytochemical techniques. Isozymes A and B of L-HOX were purified from rat liver and kidney, respectively. The apparent molecular weights of the subunits of the isozymes A and B were 35,800 and 33,500 daltons, respectively, by a slab gel electrophoresis. Antibodies to the isozymes were raised in rabbits. Anti(isozyme A) is not cross-reactive with the isozyme B and vice versa anti(isozyme B) not with the isozyme A. Using anti-isozyme B, semithin sections of Epon-embedded material and ultrathin sections of Lowicryl K4M-embedded material were stained by immunoenzyme and protein A-gold techniques, respectively. By light microscopy, fine discrete granular staining was noted in proximal tubules, but not in distal tubules including thick and thin limbs of Henle and collecting tubules. By electron microscopy, gold particles representing the antigen sites for L-HOX B were confined exclusively to peroxisomes, in which most of the gold particles were localized in electron dense peripheral matrix, but little in central matrix with low electron density. The results indicate that L-HOX B does not homogeneously distribute in peroxisomes of rat kidney but might be associated with some substructure within peroxisome matrix.