Rat liver peroxisomes contain a beta-oxidation system different from that present in the mitochondria. Intermediates in this oxidation have not hitherto been identified by direct methods. Incubation of linoleic acid with isolated peroxisomes (in the absence of detergent) resulted in the accumulation of polar products in addition to the chain-shortened products. Omission of NAD in the incubation mixture considerably increased the accumulation of these products. Two of the products were isolated and characterized by gas chromatography-mass spectrometry. They were identified as 2,3-dehydrolinoleic acid and 3-hydroxylinoleic acid, based on identical chromatographic behaviour and mass spectra compared to synthetic reference compounds. Stereochemical analysis of catalytically hydrogenated 3-hydroxylinoleic acid showed a D/L ratio near to one. The mechanism behind the apparent lack of stereospecificity is discussed in relation to the recently described novel peroxisomal 2-enoyl-CoA hydratase (Smeland, T.E., Li, J., Chu, C.-h., Cuebas, D. and Schultz, H. (1989) Biochem. Biophys. Res. Commun. 160, 988-992 and Hiltunen, J.K., Palosaari, P.M. and Kunau, W.-H. (1989) J. Biol. Chem. 264, 13536-13540). In previous work we have demonstrated that beta-oxidation intermediates accumulate also in the peroxisomal metabolism of C27-bile acid intermediates and prostaglandins. The possibility is discussed that the peroxisomal beta-oxidation system is less tightly coupled than the corresponding system in mitochondria.