The microsomal triglyceride transfer protein (MTP) is essential for the synthesis and secretion of apoB-containing lipoproteins. We investigated the role the MTP -493G/T gene polymorphism in determining the apoB-100 secretion pattern and LDL heterogeneity in healthy human subjects. Groups of carriers of the T and the G variant (n=6, respectively) were recruited from a cohort of healthy, 50-year-old men. Kinetic studies were performed by endogenous d₃-Leucine labelling of apoB and subsequent quantification of the stable isotope incorporation. ApoB production rates, metabolic conversions and eliminations were calculated by multicompartmental modelling (SAAM-II). LDL subfraction distribution was analyzed in the entire cohort (n=377). Carriers of the MTP-493T allele had lower plasma LDL apoB and lower concentration of large LDL particles (LDL-I: 136±57 (TT) vs. 175±55 (GG) mg/L, p<0.01). Kinetic modelling suggested that MTP-493T homozygotes had 60% lower direct production rate of intermediate density lipoprotein (IDL)+ LDL compared with homozygotes for the G allele (p<0.05). No differences were seen in production rates of large and small VLDL, nor were there any differences in metabolic conversion or elimination rates of apoB between the genotype groups. This study shows that a polymorphism in the MTP gene affects the spectrum of endogenous apoB-containing lipoprotein particles produced in humans. Reduced direct production of LDL+IDL appears to be related to lower plasma concentrations of large LDL particles.