The pathways of peroxisomal and mitochondrial fatty acid oxidation were monitored with the use of substrates which produce (NADH)-H-3. I used as marker substrates: D-[3-H-3]3-hydroxybutyrate for mitochondrial (NADH)-H-3 production, [2-H-3]glycerol for cytosolic (NADH)-H-3 production, and [2-H-3]acetate to measure carbon-bound H-3 which was also generated by the metabolism of the commercial 9,10-H-3-labelled fatty acids. The assumption that peroxisomal (NADH)-H-3 can be considered to be equivalent to cytosolic (NADH)-H-3 was supported using a specific inhibitor of mitochondrial fatty acid oxidation. The approach involves determination of the specific yields, and the relative distribution on carbons 4 and 6, of H-3 in glucose from the marker substrates and the labelled fatty acids. In hepatocytes from clofibrate-treated rats, the amount of palmitate or oleate oxidation which starts in the peroxisomes is comparable with that which starts in the mitochondria.