A flow cytometric study was performed on the liver of normal and clofibrate-treated rats. The flow cytometric patterns of these fractions showed three distinct populations (R1, R2 and R3). The R3 region was remarkably increased in the clofibrate-treated nuclear fraction, and was applied to sucrose linear density gradient centrifugation. Mt1, Mt2, Mt3 and Mt4 fractions were isolated and reacted with rhodamine-123. An essential enzyme for beta-oxidation, delta 3, delta 2-enoyl-CoA isomerase, was mainly expressed in Mt1 of the control-nuclear fraction, but not in Mt1, Mt2 and Mt4 in the clofibrate-treated nuclear fraction. These results suggest that clofibrate affects the flow cytometrical population of the mitochondria and changes the expression level of beta-oxidation enzyme(s) of the mitochondria in rat liver.