Low density lipoprotein (LDL) particle size is a genetically influenced trait associated with coronary heart disease (CHD). This study investigates the effects of genetic variation in plasma factors with important roles in lipoprotein metabolism on LDL heterogeneity. Common variants in the cholesteryl ester transfer protein (CETP-629C/A), lipoprotein lipase (LPL S447X), hepatic lipase (HL-480C/T) and apolipoprotein E (apoE e2/e3/e4) genes were studied in relation to LDL particle size distribution in 377 healthy, middle-aged men. A high-resolution polyacrylamide gradient gel electrophoresis technique was used to measure plasma concentrations of four LDL subfractions. The CETP-629A and LPL 447X alleles were associated with moderately increased LDL peak particle size. In contrast, the apoE e4 allele was associated with a marked reduction in LDL peak particle size and an increased relative proportion and plasma concentration of small, dense LDL. An interaction between the HL-480C/T and apo E polymorphisms contributed significantly to increased plasma concentration of small, dense LDL (LDL-III) in HL-480T carriers. In summary, the investigated polymorphisms were associated with diverse effects on the LDL particle size distribution, consistent with respect to protein function and proposed association with CHD risk. The observed associations were further modulated by gene-gene and gene-environment interactions.