Microsomal triglyceride transfer protein (MTP) is a heterodimer consisting of the multifunctional enzyme protein disulfide isomerase and a unique, large 97-kDa subunit. MTP is required for the assembly and secretion of very low density lipoproteins and chylomicrons by the liver and intestine, respectively. In vitro, MTP catalyzes the transport of triglyceride, cholesteryl ester, and phosphatidylcholine between phospholipid surfaces. We have characterized the gene encoding the large subunit of human MTP. It contains 18 exons and spans approximately 55-60 kb. Fluorescent in situ hybridization localized this gene to band 4q24 of chromosome 4. A (CA)n repeat polymorphic marker, which may be useful for investigating a link between the MTP gene and genetic defects in lipid metabolism, was identified in intron 10. Sequence analysis of the 5' flanking region of the gene revealed potential sites which may bind transcriptional factors and control MTP expression.