When measuring breath-by-breath (BbB) oxygen uptake at the mouth (V MO2 ) as the difference between the amount of inspired and expired oxygen, BbB variation in lung oxygen stores due to BbB variation in end-expiratory lung volume (VLET) introduces an error leading to a decreased signal-to-noise ratio when compared to oxygen uptake at the alveolo-capillary interface (V AO2 ). Conventional BbB measurement of oxygen uptake does not measure BbB changes in lung oxygen stores. Opto-electronic plethysmography(OEP) allows accurate monitoring of absolute lung volume changes and BbB quantification of change in pulmonary oxygen stores. To quantify BbB variation of lung oxygen stores and to assess variability in V MO2 due to BbB variation of lung oxygen stores, we measured, V MO2 and V AO2 in parallel, at rest,during transients and during steady state cycling exercise at 60, 90 and 120W in 7 healthy male subjects. Average V MO2 and V AO2 at steady state were not different (p = 0.328).Direct measurement of V AO2 reduced overall BbB variability by 24% (p < 0.0001) and variance of the difference between V MO2 and V AO2 could be explained for 55% by BbB changes in VLET and expiratory oxygen fraction. V AO2 was higher than V MO215 and 30 s after exercise onset (p < 0.01). We conclude that (1) by taking into account changes in lung oxygen stores BbB variability of oxygen uptake is reduced, (2) alveolar oxygen stores change rapidly during transients to exercise, and (3) changes in alveolar oxygen stores affect BbB oxygen uptake measured at the mouth during the cardio-dynamic phase I.