The effects of concurrent hypoxic/endurance training on mitochondrial respiration in permeabilized fibers in trained athletes were investigated. Eighteen endurance athletes were divided into two training groups: normoxic (Nor, n = 8) and hypoxic (H, n = 10). Three weeks of endurance training (5 sessions of 1h-1h30 week^-1) were completed. All training sessions were performed under normoxic (160 mmHg P_IO₂) or hypoxic conditions (100 mmHg P_IO₂, 3000 m) for Nor and H group respectively at the same relative intensity. Prior to and after the training period, an incremental test to exhaustion in normoxia was performed and muscle biopsy samples were taken from the vastus lateralis and mitochondrial respiration in permeabilized fibers was measured. Peak power output (PPO) increased by 7.2% and 6.6% (P < 0.05) for Nor and H respectively, whereas VO_2max remained unchanged: 58.1 ± 0.8 vs. 61.0 ± 1.2 ml.kg-1.min-1 and 58.5 ± 0.7 vs. 58.3 ± 0.6 ml^.kg^-1.min^-1 for Nor and H respectively between W0 and W4. Maximal ADP-stimulated mitochondrial respiration (Vmax) significantly increased for glutamate + malate (6.27 ± 0.37 vs. 8.51 ± 0.33 nmolO₂^.min^-1.mg^-1dry weight), and significantly decreased for palmitate + malate (3.88 ± 0.23 vs. 2.77 ± 0.08 nmolO₂^.min^-1.mg^-1dry weight) in H group. In contrast, no significant differences were found for Nor group. The findings demonstrate that: 1) a three-week training period increased the PPO at sea-level without any changes in VO_2max and 2) a three-week hypoxic exercise training seems to alter the intrinsic properties of mitochondrial function, i.e. substrate preference.