Recently, 2 new enzyme deficiencies of equine skeletal muscle have been identified, involving either mitochondrial respiration or glycolysis. We hypothesised that in these unique horses, maximum oxygen consumption (V̇O2max) would not be limited by oxygen transport but rather by oxygen utilisation and substrate metabolism, respectively. To test this hypothesis, an Arabian mare with Complex I deficiency (OXID) and 2 half-sibling Quarter Horses with a polysaccharide storage myopathy (GLY1 and GLY2) were accommodated to run at maximal speed on a treadmill. These horses and 5 healthy Thoroughbred horses each performed 2 identical exercise tests consisting of 6 min submaximal exercise and 2 min at their maximal speed. The OXID horse fatigued at 6 m/s with a markedly low V̇O2max (20% of controls), a low maximum total power output (25% of controls) with a high contribution of net anaerobic power (38% compared to 24% for controls). The GLY horses developed a stiff gait and fatigued with a low V̇O2max (50–65 % of controls), a low maximum total power (50–60% of controls) but with a low contribution of net anaerobic power (18% vs. controls 24%). The rate of lactate accumulation at maximal speeds was approximately 30–50% lower than for controls. It appeared that mitochondrial oxidative capacity severely limited aerobic performance in the OXID horse and substrate limitation within the Embden Myerhof pathway limited both aerobic and anaerobic power output in the GLY horses. We conclude that in some horses, skeletal muscle oxidative or glycolytic capacity may limit maximum aerobic performance.