Dihydroxyacetone phosphate acyltransferase (DHAP-AT) and alkyldihydroxyacetone phosphate synthase (DHAP-synthase) activities were examined in subcellular fractions of rat liver. The results indicate that at least 80% of DHAP-AT (assays carried out at pH 5.4) activity in rat liver is in peroxisomes, and the remaining activity is mitochondrial. In contrast to DHAP-AT, DHAP-synthase was detected in all subcellular fractions analyzed but the activity in peroxisomes was 208-fold and 42-fold greater compared to mitochondria and microsomes, respectively. We estimate that at least 70% of the DHAP-synthase activity in rat liver is in peroxisomes. DHAP-AT and DHAP-synthase activities were also examined in homogenates of skin fibroblasts from patients with inherited defects in peroxisomal structure and/or function. Both the enzyme activities were deficient in Zellweger syndrome whereas the activities were only partially deficient in infantile Refsum's disease. Greater reduction in DHAP-synthase activity, but only a partial reduction in DHAP-AT activity was observed in rhizomelic chondrodysplasia punctata. However, both DHAP-AT and DHAP-synthase activities were either normal or near normal in Refsum's disease or X-linked adrenoleukodystrophy. The results reported suggest that various peroxisomal disease states can be identified based on DHAP-AT and DHAP-synthase activities in skin fibroblasts of patients.