Sterol carrier protein 2 (SCP2; also called nonspecific lipid transfer protein) is a small basic sterol carrier and lipid transfer protein assumed to participate in the intracellular transport of sterols and certain other lipids. Upon cloning and sequencing SCP2-encoding cDNAs, we and others found cDNAs containing unexpected in-frame 5'-extensions of up to 1,250 nucleotides upstream of the initiator ATG of the cDNA encoding pre-SCP2. The corresponding transcripts are primarily expressed in the liver and are predicted to encode a previously undescribed fusion protein containing a 143-amino acid C-terminal domain completely identical to pre-SCP2 and a 404-amino acid N-terminal domain with unknown biochemical activity or function (named sterol carrier protein x, SCPx). Here, we show that purified recombinant SCPx cleaves 3-oxoacyl(n)-CoA to yield acetyl-CoA and acyl(n-2)-CoA. Like SCP2, recombinant SCPx also stimulates the microsomal conversion of 7-dehydrocholesterol to cholesterol and transfers phosphatidylcholine and 7-dehydrocholesterol from small unilamellar vesicles to acceptor membranes in vitro. Furthermore, SCPx epitopes are primarily detected within peroxisomes. These findings suggest that SCPx is a previously undescribed peroxisomal 3-ketoacyl-CoA thiolase (EC 2.3.1.16) with intrinsic sterol carrier and lipid transfer activity (suggested name: SCP2/3-oxoacyl-CoA thiolase).