The effects of riboflavin deficiency on mitochondrial and peroxisomal substrate oxidation were examined in young (treatment begun at weaning) and adult Sprague-Dawley rats that were fed diets low and high in fat. State 3 respiration rates (ADP-stimulated) were used as an estimate of mitochondrial oxidation rates. The oxidation of palmitoyl-CoA and palmitoylcarnitine, and to a lesser extent, glutamate, pyruvate and succinate, by hepatic mitochondria isolated from the young rats was depressed with riboflavin deficiency. There was no effect of dietary fat level on mitochondrial substrate oxidation. Carnitine palmitoyltransferase-A (CPT-A) V(max) was increased with riboflavin deficiency and with increasing dietary fat. Cyanide-insensitive palmitoyl-CoA oxidation was used to estimate peroxisomal palmitate oxidation. Expressed as total hepatic capactiy, peroxisomal palmitate oxidation was depressed with riboflavin deficiency. This effect was the result of the reduced feed intake rather than riboflavin deficiency per se. Increasing dietary fat resulted in increased peroxisomal palmitate oxidation. Starvation of young rats did not change mitochondrial oxidation rates, although riboflavin-deficient starved rats exhibited increased rates of palmitoyl-CoA oxidation as well as increased CPT-A V(max). In adult rats, after 5 wk of deficiency, only palmitoyl-CoA and palmitoylcarnitine oxidation rates were depressed. Dietary fat level did not interact with riboflavin deficiency. However, CPT-A V(max) was increased with riboflavin deficiency and with increased dietary fat level. Further, depressed hepatic fatty acid oxidation can occur in adult rats as a sequel to the feeding of riboflavin-deficient diets.