A 16-year-old boy with a two-year history of recurrent attacks of myalgia, muscle cramps without weakness, and myoglobinuria was shown to have a deficiency in muscle carnitine palmityltransferase. Serum concentrations of creatinine phosphokinase, serum glutamic oxalacetic transaminase, and aldolase were elevated. An electromyogram was consistent with a nonspecific myopathy as were microscopic and ultrastructural examinations of biopsied muscle. Venous lactic acid response to ischemic exercise was compatible with paroxysmal idiopathic myoglobinuria. Activities of muscle phosphorylase A and B, phosphofructokinase, muscle palmityl CoA synthetase, carnitine, and serum carnitine were normal as was the glycogen content. Activity of muscle carnitine palmityltransferase (2.7 microM/minute/mg protein), as measured by a spectrophotometric method and by radioactive assay, was significantly reduced when compared to normal control subjects (14.5 microM/minute/mg protein) and ischemic control subjects (13.8 microM/minute/mg protein). Muscle carnitine acetyltransferase (13.4 microM/minute/mg protein) was approximately 50% of normal control values (25.5 microM/minute/mg protein). This is the third reported case of myoglobinuria in a patient associated with a deficiency of muscle carnitine palmityltransferase activity.