We investigated the association between histologically defined atherosclerotic lesions in the carotid arteries and the genetic variants of APOE and LPL in a population-based sample of Finns aged 85 or over. Post-mortem analysis of carotid arteries was performed in 240 subjects. Atherosclerotic lesions were categorized according to the modified American Heart Association criteria, and classified into four different categories: pathological intimal thickening (PIT), fibrous cap atheromas (FCA), calcified lesions (CL), and atherosclerotic burden (AB) (a combination of the other three categories). APOE epsilon4 genetic variant was associated with PIT (p=0.018) and AB (p=0.006) in the carotid arteries, and its effect was independent of the serum lipid levels. The genetic variant LPL Ser447Ter was protective against FCA (p=0.031) and AB (p=0.012), while APOE epsilon2 was protective against FCA (p=0.035). Our results suggest that the APOE epsilon4, epsilon2 and LPL Ser447Ter variants may have different roles in the atherosclerotic process and their effects are seen even in the oldest old population.