The expression of the sterol-carrier protein 2 (SCP-2)-encoding gene (SCP-2) is unusually complex. At least four SCP-2-related transcripts are detected in mouse liver: two, of 1.6 and 3.0 kb, are expressed to high levels while the other two, of 0.9 and 2.2 kb, reveal relatively low expression. Hybridization with a probe which specifically hybridizes with the rat SCP-2-related cDNA encoding rat SCP-x reveals that the 2.2- and 3.0-kb transcripts encode mouse SCP-x. SCP-x transcripts are expressed predominantly in the liver, but low-level expression can be demonstrated in all tissues analyzed. Isolation and characterization of two overlapping SCP-x cDNAs indicate that the cDNAs are derived from alternatively polyadenylated transcripts spanning approx. 2.2 and approx. 2.9 kb. Nucleotide sequencing reveals that the predicted ORF, which consists of 547 codons, is composed of 143 C-terminal amino acids which are essentially identical with mouse pre-SCP-2 and 404 N-terminal residues which are specific for SCP-x. To date, it is not clear if all SCP-2-related transcripts are transcribed from a single gene. We have isolated a genomic clone containing an SCP-2-related pseudogene which has some of the characteristics expected for a truncated processed pseudogene. Therefore, our results indicate that at least some of the multiple restriction fragments which are detected by Southern hybridization analyses with SCP-x cDNA-derived probes can be explained by cross-hybridization with a pseudogene.