Mitochondrial muscle alterations are common in patients with chronic obstructive pulmonary disease (COPD) and manifest mainly as decreased oxidative capacity and excessive production of reactive oxygen species (ROS). The significant loss of oxidative capacity observed in the quadriceps of COPD patients is mainly due to reduced mitochondrial content in the fibers, a finding consistent with the characteristic loss of type I fibers observed in that muscle. Decreased oxidative capacity does not directly limit maximum performance; however, it is associated with increased lactate production at lower exercise intensity and reduced endurance. Since type I fiber atrophy does not occur in respiratory muscles, the loss of such fibers in the quadriceps could be to the result of disuse. In contrast, excessive production of ROS and oxidative stress are observed in both the respiratory muscles and the quadriceps of COPD patients. The causes of increased ROS production are not clear, and a number of different mechanisms can play a role. Several mitochondrial alterations in the quadriceps of COPD patients are similar to those observed in diabetic patients, thus suggesting a role for muscle alterations in this comorbidity. Amino acid metabolism is also altered. Expression of peroxisome proliferator-activated receptor-γ coactivator-1α mRNA is low in the quadriceps of COPD patients, which could also be a consequence of type I fiber loss; nevertheless, its response to exercise is not altered. Patterns of muscle cytochrome oxidase gene activation after training differ between COPD patients and healthy subjects, and the profile is consistent with hypoxic stress, even in nonhypoxic patients.