The aim of the present study is to investigate whether microsatellite instability (MSI) and loss of heterozygosity (LOH) are involved in atherogenesis. Paraffin-embedded tissues of thoracic and abdominal aortas were collected from 29 non-neoplastic autopsied cases. We selected two types of atherosclerotic lesions including fibrocellular intimal thickening and uncomplicated atheromatous lesions, and analyzed two sites such as the aortic tunica intima and tunica media in each case. The frequencies of MSI and LOH were highest in the aortic tunica intima of atheromatous lesions and lowest in the aortic tunica media of fibrocellular intimal thickening lesions. Our results suggest that genetic instabilities such as MSI and LOH may be involved in the development of atherosclerotic lesions.