The muscles of four infants with cerebro-hepato-renal (Zellweger) syndrome were studied during life and/or at necropsy. A mitochondrial myopathy was demonstrated, similar to mitochondrial alterations demonstrated in liver and brain in this disease. Muscle fibers with red-staining subsarcolemmal aggregates were identified with Gomori trichrome stain in two cases. Subsarcolemmal and intermyofibrillar zones of increased concentrations of NADH-TR, SDH, and cytochrome-c-oxidase activity were demonstrated histochemically in all four cases. Degenerative and cytoarchitectural changes in muscle fibers were not found. Ultrastructural studies showed large aggregates of mitochondria and increased lipid in the subsarcolemmal and intermyofibrillar spaces. Degenerative changes in mitochondria and lipid also were demonstrated, but paracrystalline inclusions were not seen. The distribution of these changes was not uniform between patients or between different muscles in the same patient. The diaphragm was affected more severely than proximal or distal muscles of the extremities. Direct involvement of muscle mitochondria in this disease may interfere with energy metabolism and contribute to the clinical findings of hypotonia, weakness, and respiratory insufficiency. The muscle biopsy with histochemistry and electron microscopy may be used as a diagnostic adjunct in suspected cases, but the variation encountered dictates dictates caution in the interpretation of negative findings.