Despite the common use of equids as visitors to high altitude mountainous environments, there are a paucity of carefully orchestrated scientific approaches. Further, again as a function of a common perceived advantage of mules over horses in these similar environments there are needs for controlled comparisons between these 2 equids. To measure haematological and respiratory function in horses and mules at low altitude (225 m), at rest and post exercise. In addition the rate and magnitude of these changes were followed over a 13 day period at high altitude (3800 m) to contrast acclimatisation. Resting and exercise venous blood samples (1 min post exercise) were obtained from 6 horses and 5 mules housed at 225 m (LA) and then transported to 3800 m (HA) for 13 days. The standardised exercise tests at both LA and HA consisted of trotting (3.0 m/sec) up an incline (6%) for 2 km. Data were analysed with repeated measures ANOVA (comparison of altitude acclimatisation and species) for changes in haematological and respiratory gases. At low altitude, no group differences were found with both resting (P = 0.69) and exercising (P = 0.74) heart rates. Resting PCV was 8% lower in the mules (P = 0.02) and 20% lower during exercise (P = 0.02). Horses had significantly higher 2,3-diphosphoglycerate (2,3-DPG)/g Hb at both rest (P = 0.003) and exercise (P = 0.03). Exercise at HA increased PCV (P = 0.03) in both groups, but the increase was attenuated in the mules compared to horses. The increase with 2,3-DPG/g Hb was expressed at HA in both groups (P = 0.001) and was also attenuated in mules (P = 0.03). Both groups were alkalotic compared to LA (P = 0.001), and there were no group differences (P = 0.95). Of the variables measured, the most notable distinction between species was identified for only PCV and 2,3-DPG with both higher in horses, at both LA and HA. While the attenuated response of PCV in mules for the same exercise might argue for an improved adaptation to altitude, the lower 2,3-DPG might not. Other variables during the exercise bout were not different between species.