One of the most important functions of peroxisomes, at least in humans, is the beta-oxidation of a range of different fatty acids and fatty acid derivatives. Recent studies have shown that the enzymatic machinery required for the beta-oxidations of these substrates, may be much more complex as originally thought. We now report that the conventional peroxisomal thiolase which has so far been thought to catalyze the thiolytic cleavage of the 3-oxoacyl-CoA esters of all fatty acids oxidized in peroxisomes, shows poor reactivity towards the 3-oxoacyl-CoA esters of 2-methyl branched-chain fatty acids such as pristanic acid. Our data further show, that SCPx, a 58 kDa protein with both thiolase and sterol carrier protein activity but unknown function so far, readily reacts with 3-oxopristanoyl-CoA. Taken together, our data show that SCPx plays a central role in branched chain fatty acid beta-oxidation in peroxisomes. This finding has major implications not only for the functional organization of the peroxisomal beta-oxidation system but also for studies dealing with the resolution of the underlying defect in patients with some defect in peroxisomal beta-oxidation.