Abstract-Small, dense LDL particles are associated with increased risk of cardiovascular disease. To identify the genes that influence LDL size variation, we performed a genome-wide screen for cholesterol concentrations in 4 LDL size fractions. Samples from 470 members of randomly ascertained families were typed for 331 microsatellite markers spaced at Ϸ15 cM intervals. Plasma LDLs were resolved by using nondenaturing gradient gel electrophoresis into 4 fraction sizes (LDL-1, 26.4 to 29.0 nm; LDL-2, 25.5 to 26.4 nm; LDL-3, 24.2 to 25.5 nm; and LDL-4, 21.0 to 24.2 nm) and cholesterol concentrations were estimated by staining with Sudan Black B. Linkage analyses used variance component methods that exploited all of the genotypic and phenotypic information in the large extended pedigrees. In multipoint linkage analyses with quantitative trait loci for the 4 fraction sizes, only LDL-3, a fraction containing small LDL particles, gave peak multipoint log 10 odds in favor of linkage (LOD) scores that exceeded 3.0, a nominal criterion for evidence of significant linkage. The highest LOD scores for LDL-3 were found on chromosomes 3 (LODϭ4.1), 4 (LODϭ4.1), and 6 (LODϭ2.9). In oligogenic analyses, the 2-locus LOD score (for chromosomes 3 and 4) increased significantly (Pϭ0.0012) to 6.1, but including the third locus on chromosome 6 did not significantly improve the LOD score (Pϭ0.064). Thus, we have localized 2 major quantitative trait loci that influence variation in cholesterol concentrations of small LDL particles. The 2 quantitative trait loci on chromosomes 3 and 4 are located in regions that contain the genes for apoD and the large subunit of the microsomal triglyceride transfer protein, respectively. . In addition to total LDL concentrations, many studies indicate that a small, dense LDL particle phenotype is also a risk factor for CVD. 1 In fact, several recent prospective studies have shown that LDL particle size phenotype is predictive of subsequent measurements of CVD. 2-4 However, these associations are not independent of other correlated traits, such as triglyceride concentration, which suggests small LDLs are a component of an atherogenic lipoprotein phenotype. 5 Possible mechanisms for a direct role of small LDLs in atherogenesis include heightened susceptibility to oxidation 6 and/or altered affinity for the LDL receptor. 7 LDL size phenotype is heritable 8 and most segregation analyses suggest the existence of a major locus for the trait. 9 -13 Attempts to identify the gene(s) that might influence LDL size phenotype have so far met with equivocal results. A quantitative trait locus (QTL) for the dichotomous trait for LDL size (pattern A or large buoyant LDLs versus pattern B or small dense LDLs) was found to be linked to the LDL receptor locus, 14 but not the apoB locus, 15,16 whereas QTLs for LDL peak particle size were reported to be linked to the genes for the LDL receptor, apoB, cholesteryl ester transfer protein, and manganese superoxide dismutase. 17,18 The evidence for these linkages has not been s...