The effects of physical exercise on the lipid profile in mitochondrial membranes of liver and skeletal muscle were examined in rats fed with virgin olive oil or sunflower oil. Thirty male Wistar rats, 21 d old, were randomly assigned to four groups according to fat ingestion and physical activity over an 8-week period. For each type of oil, one group acted as a control group while rats from the other were trained to run for 40 min daily on a horizontal treadmill, at a speed of 35 m/min. The results show that diet affected the fatty acid profile of the mitochondrial membranes from skeletal muscle and liver. Physical exercise also modified the fatty acid profile of the mitochondrial membranes. Total monounsaturated fatty acids decreased (P < 0.001) in liver mitochondria of exercised animals. Total polyunsaturated fatty acids in mitochondrial membranes of liver increased (P < 0.005) after exercise but those in mitochondrial membranes of skeletal muscle decreased (P < 0.05). These changes due to the exercise may arise via several mechanisms, e.g. fluidity regulation; changes in the eicosanoid metabolism; differences in the availability or oxidation rate of the different fatty acids.