Accurate assessment of energy expenditure (EE) is important in guiding nutritional therapy but current methods are unsatisfactory. This study compared the oral 13 C-bicarbonate tracer (BT) technique using the IRIS ® system (Wagner, Germany) against indirect calorimetry (IC, ventilated-hood) to measure CO 2 output (VCO 2 ) and thus estimate EE.Ten overnight-fasted healthy male volunteers were randomised to studies at rest or mild exercise in a crossover manner. During each study BT-IRIS ® and IC were used simultaneously to measure VCO 2 and thus EE. Participants ingested a drink labelled with 50 mg 13 C-bicarbonate and breath samples were collected every 5 min for 180 min and analysed using IRIS ® . Bland–Altman plots were used to assess agreement between the two techniques in measurements of VCO 2 (L/day) and estimates of EE (kJ/day).Mean ± SE age and BMI of participants were 21.1 ± 1.1 yrs and 23.6 ± 0.6 kg/m 2 . Both at rest and exercise, there was small bias but overall poor agreement between the two techniques as evident by the wide 95% limits of agreement in measurements of VCO 2 and EE: rest VCO 2 (bias 1.4, SD 93, 95% limits of agreement −180 to 183), rest EE (−8.3, 1830, −3595 to 3578), exercise VCO 2 (49.3, 66.1, −80.4 to 178.9) and exercise EE (1083, 1944, −2727 to 4893). Furthermore, there was also evidence of systematic error in these measurements.Prior to clinical application, further optimisation of the BT-IRIS ® system should be undertaken, given the poor agreement with IC in measuring VCO 2 and estimating EE.