Abstract Objectives: To evaluate the association between plasma lipids and insulin and variation in the genes for apolipoproteins ( APO) E (CfoI), B (insertion/deletion), C1 (HpaI), and C3 (C-482T, C3238G) in a population-based Czech Slavonic study. Design and methods: In 131 men and 154 women, polymorphisms were investigated using PCR. In the same subjects plasma lipid levels and insulin were measured. Results: In the women, carriers of the e4 allele had higher apoB ( p = 0.03) and triglyceride ( p = 0.03) compared to e3 homozygotes, whereas in the men, the effect of the e4 allele was seen on total cholesterol ( p = 0.02), LDL cholesterol ( p = 0.003) and apoB ( p = 0.001). Compared with SP27 (insertion) homozygotes of the APOB polymorphism, women SP24 (deletion) homozygotes had higher levels of total ( p = 0.003) and LDL cholesterol ( p = 0.007) and apoB ( p = 0.05). No significant effect was seen in the men. Women homozygous for the APOC3 –482T allele had higher insulin levels than –482C homozygotes ( p = 0.03). Men homozygous for APOC3 –482T allele have the highest plasma triglyceride level ( p = 0.02). The APOC1 polymorphism exhibited no significant effect on any of the parameters studied. Conclusions: In this sample, variation at the APOE, APOB and APOC3 genes play a role in determining plasma levels of insulin and lipids, and emphasize the importance of gender-associated effects in the genetic determinations.