Limited validation research exists for applications of breath-by-breath systems of expired gas analysis indirect calorimetry (EGAIC) during exercise. We developed improved hardware and software for breath-by-breath indirect calorimetry (NEW) and validated this system as well as a commercial system (COM) against 2 methods: (i) mechanical ventilation with known calibration gas, and (ii) human subjects testing for 5 min each at rest and cycle ergometer exercise at 100 and 175 W. Mechanical calibration consisted of medical grade and certified calibration gas ((4.95% CO2, 12.01% O2, balance N2), room air (20.95% O2, 0.03% CO2, balance N2), and 100% nitrogen), and an air flow turbine calibrated with a 3-L calibration syringe. Ventilation was mimicked manually using complete 3-L calibration syringe manouvres at a rate of 10Â·min'1 from a Douglas bag reservoir of calibration gas. The testing of human subjects was completed in a counterbalanced sequence based on 5 repeated tests of all conditions for a single subject. Rest periods of 5 and 10 min followed the 100 and 175 W conditions, respectively. COM and NEW had similar accuracy when tested with known ventilation and gas fractions. However, during human subjects testing COM significantly under-measured carbon dioxide gas fractions, over-measured oxygen gas fractions and minute ventilation, and resulted in errors to each of oxygen uptake, carbon dioxide output, and respiratory exchange ratio. These discrepant findings reveal that controlled ventilation and gas fractions are insufficient to validate breath-by-breath, and perhaps even time-averaged, systems of EGAIC. The errors of the COM system reveal the need for concern over the validity of commercial systems of EGAIC.