OBJECTIVE: To examine two different protocols for measurement of metabolic rate (MR) in children. DESIGN: MR was first measured under typical basal conditions employed in adults and then compared to an alternative protocol in which the measurements were performed in post-prandial state. Repeat measurements were performed for the post-prandial protocol. SUBJECTS: The cross-over study was performed in 19 healthy children, and the reliability data were provided from 169 observations in children. All children were 4-9 years of age. MEASUREMENTS: Basal MR was measured in the morning in the fasted state after children spent the night at The Clinical Research Center. Measurements were repeated 2 weeks later after children reported to the laboratory after consuming their normal breakfast at home (post-prandial). Body composition was measured using bioelectrical resistance. RESULTS: MR was ~ 11% higher under post-prandial conditions (1165 ± 151 kcal/day vs 1050 ± 151 kcal/day; p < 0.001 by paired t-test). Respiratory quotient (RQ) was ~ 3% higher under post prandial conditions (0.94 ± 0.03 vs 0.91 ± 0.05; p < 0.001 by paired t-test). The correlation between MR and fat free mass was stronger when measurements were performed under post-prandial (r = 0.88; p < 0.001) vs basal conditions (r = 0.64; p < 0.005). The coefficient of variation for 169 repeat measurements using the post-prandial protocol averaged 5.4 ± 4.1% for MR and 2.9 ± 2.2% for RQ. CONCLUSIONS: The stronger correlation between MR and fat free mass during post prandial measurements implies that the less stringent testing conditions improves compliance during measurement and provides the environment for reproducible measurements. We propose an alternative protocol for determination of post-prandial metabolic rate in children that is reliable, practical and can be potentially applied in a clinical setting.