High intensity exercise is associated with production of energy by both aerobic and anaerobic metabolism. Conditioning by repeated exercise increases the maximal rate of aerobic metabolism, aerobic capacity, of horses, but whether the maximal amount of energy provided by anaerobic metabolism, anaerobic capacity, can be increased by conditioning of horses is unknown. We, therefore, examined the effects of 10 weeks of regular (4–5 days/week) high intensity (92 ± 3 %V̇O2max) exercise on accumulated oxygen deficit of 8 Standardbred horses that had been confined to box stalls for 12 weeks. Exercise conditioning resulted in increases of 17% in V̇O2max (P<0.001), 11% in the speed at which V̇O2max was achieved (P = 0.019) and 9% in the speed at 115% of V̇O2max (P = 0.003). During a high speed exercise test at 115%V̇O2max, sprint duration was 25% longer (P = 0.047), oxygen demand was 36% greater (P<0.001), oxygen consumption was 38% greater (P<0.001) and accumulated oxygen deficit was 27% higher (P = 0.040) than values before conditioning. VLa4 was 33% higher (P<0.05) after conditioning. There was no effect of conditioning on blood lactate concentration at the speed producing V̇O2max or at the end of the high speed exercise test. The rate of increase in muscle lactate concentration was greater (P = 0.006) in horses before conditioning. Muscle glycogen concentrations before exercise were 17% higher (P<0.05) after conditioning. Exercise resulted in nearly identical (P = 0.938) reductions in muscle glycogen concentrations before and after conditioning. There was no detectable effect of conditioning on muscle buffering capacity. These results are consistent with a conditioning-induced increase in both aerobic and anaerobic capacity of horses demonstrating that anaerobic capacity of horses can be increased by an appropriate conditioning programme that includes regular, high intensity exercise. Furthermore, increases in anaerobic capacity are not reflected in blood lactate concentrations measured during intense, exhaustive exercise or during recovery from such exercise.