The objective of the study was to determine the value of indirect calorimetry and nitrogen balance (N balance) in order to evaluate the current feeding protocols of mechanically ventilated children. The study was designed as a cross-sectional prospective study. In 36 mechanically ventilated children energy expenditure was measured by indirect calorimetry, and total urinary nitrogen excretion (TUN) was determined. Substrate utilization and respiratory quotient (RQ) were calculated from the measured values of oxygen consumption (VO2), carbon dioxide production (VCO2), and TUN. The RQ was compared with the RQ of the macronutrients administered (RQmacr) according to the modified criteria of Lusk. In results, the total measured energy expenditure (TMEE) showed a wide variation (range 155-272 kJ.kg-1.d-1). The N balance was positive in 20 and negative in 16 patients. The ratio of caloric intake/TMEE was significantly higher in patients with a positive N balance (1.50 +/- 0.06) as compared with those with a negative N balance (0.8 +/- 0.1, P < 0.001). There was a significant relationship between the difference of RQ-RQmacr versus the ratio caloric intake/TMEE (r = 0.72, P < 0.001). Carbohydrate and fat utilization were not significantly different in patients with a positive or negative N balance. Protein utilization was significantly higher in those patients with a negative N balance. We concluded that measurement of TMEE with indirect calorimetry results in accurate determination of energy needs in critically ill mechanically ventilated children. Feeding according to or in excess of the TMEE is correlated with a positive N balance. A combination of the RQ and the RQmacr can be helpful in differentiating under- or overfeeding.