To determine clinical, anthropometric, metabolic, and nutritional factors affecting nitrogen balance somatic protein status and substrate utilization in critically ill children measured energy expenditure (MEE) was measured by indirect calorimetry within 24 hr of an acute illness, solid organ transplantation, or cardiovascular surgery. Predicted basal metabolic rate was calculated using the Schofield equation. Somatic protein was estimated by the creatinine-height index. Nitrogen balance (NB) was calculated by subtracting the total nitrogen input from output. The net substrate (fat, carbohydrate, and protein) oxidation rates were calculated using the Weir formula modified by Frayn. Sixty-eight NB studies, indirect calorimetric and anthropometric measurements performed in 37 patients. Nitrogen balance was worse when the MEE/Predicted basal metabolic rate ratio was < 0.9 or > 1.1. The incidence of negative NB was 91% when the caloric intake was less than MEE and 9% when it was equal to or greater than MEE (P < 0.05). On day 1, 27% had mild to moderate somatic protein depletion and 5.4% had severe somatic protein depletion. Only the persistence of stress and co-morbidity were associated with the creatinine-height index (P < 0.001). Without Multiple Organ System Failure (MOSF), there was a trend toward positive nitrogen balance by day 7 while with MOSF, negative nitrogen balance persisted even by day 7 (P < 0.05). When caloric intake was less than MEE, mean substrate utilization was 48.6% from lipid, 37.1% from carbohydrate, and 14.3% from proteins. But, when caloric intake was greater than MEE, mean substrate utilization was 83.3% from carbohydrate and 16.7% from protein. Significant negative nitrogen balance and somatic protein depletion develops in critically ill pediatric patients, especially when they are inadequately fed, develop MOSF, or have previous chronic illness. Caloric intake and MOSF independently affect substrate utilization.