Aerobic training can be effective in patients with mitochondrial myopathies (MM) and McArdle’s disease (McA). The aim of the study was to use noninvasive functional evaluation methods, specifically aimed at skeletal muscle oxidative metabolism, to evaluate the effects of an aerobic exercise training (cycle ergometer, 12 wk, 4 days/wk, 65-70% of maximal heart rate) in 6 MM and 7 McA. Oxygen uptake and skeletal muscle vastus lateralis fractional O2 extraction by near-infrared spectroscopy were assessed during incremental and low-intensity constant work rate (CWR) exercises before (BEFORE) and at the end (AFTER) of training. Peak O2 uptake increased significantly with training both in MM [14.7 1.2 vs. 17.6 1.4 mlkg1min1 (mean SD)] and in McA (18.5 1.8 mlkg1min1 vs. 21.6 1.9). Peak skeletal muscle fractional O2 extraction increased with training both in MM (22.0 6.7 vs. 32.6 5.9%) and in McA (18.5 6.2 vs. 37.2 7.2%). During low-intensity CWR in both MM and McA: V ? O2 kinetics became faster in AFTER, but only in the patients with slow V ? O2 kinetics in BEFORE; the transient overshoot in fractional O2 extraction kinetics disappeared. The level of habitual physical activity was not higher 3 mo after training (FOLLOW-UP vs. PRE). In MM and McA patients a homebased aerobic training program significantly attenuated the impairment of skeletal muscle oxidative metabolism and improved variables associated with exercise tolerance. Our findings indicate that in MM and McA patients near-infrared spectroscopy and V ? O2 kinetics can effectively detect the functional improvements obtained by training.