The oxidized (UQ(ox)) and reduced (UQ(red)) forms of ubiquinone (UQ) homologues in rat tissues and subcellular fractions were analyzed to elucidate their distribution and physiological role. UQ-9 and UQ-10 were detected in all tissues studied, and UQ-9 was the predominant homologue. The total amount of UQ(ox)-10 and UQ(red)-10 was 20-50% that of UQ(ox)-9 and UQ(red)-9. The levels of these homologues were highest in heart with lesser amounts occurring in kidney, liver and other organs. In liver and blood plasma, the UQ(red) homologue amounted to 70-80% of the total UQ (UQ(ox) + UQ(red) = t-UQ). UQ(red) Was less than 30% of t-UQ in other tissues and blood cells. t-UQ was much higher in leukocytes and platelets in blood than in erythrocytes. In erythrocytes, t-UQ was exclusively located in the cell membranes. UQ(ox) and UQ(red) were also found in all subcellular fractions isolated from liver and kidney in about the same ratio as UQ(red)/t-UQ was present in the whole organ. The levels of UQ(ox) and UQ(red) per mg protein in subcellular fractions from liver were highest in mitochondria, with lesser amounts present in plasma membranes, lysosomes, Golgi complex, nuclei, microsomes and cytosol. In the mitochondria, the outer membranes were richer in t-UQ than the inner membranes. In the Golgi complex, the light and intermediate fractions were rich in t-UQ when compared to the heavy fraction. The possible physiological role of UQ(ox) and UQ(red) in tissues and subcellular fractions is discussed.