Routine exercise is widely recognized as cardioprotective. Exercise induces a variety of effects within the cardiovasculature including decreased mitochondrial damage and improved aerobic capacity. It has been generally thought that the transient increase in oxidative stress associated with exercise initiates cardioprotective processes. Somewhat paradoxically, increased oxidative stress associated with CVD risk factors is thought to play an important role in the promotion and development of cardiovascular disease (CVD). Hence, it is possible that CVD risk factors which increase oxidative stress (e.g. hypercholesterolemia) may modulate the cardioprotective effects of exercise. In this regard, the interaction between CVD risk factors and exercise on atherosclerotic lesion development and basal oxidant load are less defined. To determine the influence of pre-existent hypercholesterolemia on the cardioprotective effects of exercise, atherosclerotic lesion formation, oxidant load, mitochondrial damage, protein nitration (3-nitrotyrosine levels), and mitochondrial enzyme activities were determined in aortic tissues from normocholesterolemic (C57 control) and hypercholesterolemic (apoE -/-) mice after 16 weeks of regular exercise. In normocholesterolemic mice, regular exercise was associated with decreased mitochondrial damage and oxidant load, and increased SOD2 and ANT activities. In contrast, exercise did not decrease endogenous oxidant load and mitochondrial damage in hypercholesterolemic mice, and did not reduce atherosclerotic lesion development. These data are consistent with the notion that CVD risk factors associated with increased oxidative stress can alter the benefits of exercise, and, that mitochondrial damage appears to be correlated with the cardiovascular effects of exercise.