X-linked phosphoglycerate kinase (PGK) deficiency is a rare disorder which affects the glycolytic pathway and leads to reduced ATP production. Clinically, PGK deficiency is often associated with nonspherocytic hemolytic anemia and symptoms caused by disturbances of the central nervous system. In addition, myopathy characterized by weakness, cramps, intolerance to exercise, and myoglobinuria has been described in a few cases. We here report on a 23-year-old man who presented with episodes of muscular weakness, cramps, rhabdomyolysis, and renal failure induced by intensive physical exercise. Biochemical analysis of muscle specimens disclosed markedly reduced PGK activity (11.5% compared to normal controls). A moderate increase of glycogen was seen in numerous muscle fibers. Mitochondria in muscle fibers and endothelial cells showed accumulations of glycogen. In muscle fibers unusually large matrix granules were present in several mitochondria. A sural nerve biopsy disclosed scattered large hypomyelinated axons without evidence of demyelination and remyelination. These findings indicate involvement of mitochondria in this case of symptomatic PGK deficiency.