The objective was to determine stress related factors and nutritional indices affecting the nitrogen balance (NB) and the creatinine height index (CHI) in critically ill children on early enteral nutrition (EEN). Seventy-one consecutively enrolled critically ill children aged 2 to 204 months, requiring prolonged mechanical ventilation, were studied. All patients were on early intragastric nutrition (Nutrison Pediatric or Standard) from day 1 (energy intake equal to 1/2, 1, 5/4, 6/4 and 6/4 of the predicted basal metabolic rate on days 1-5, respectively). Nitrogen balance and CHI changes determined efficacy. Study patients had severe depletion of somatic protein status on stress day 1 (CHI <60%) but they reached the normal range of somatic protein status at the end of the EEN, on post-stress day 5 (CHI >80%, p <.004). On day 1, none of the patients had positive NB but after 5 days of EEN, 44 (62%) had positive NB and only 27 (38%) had negative NB (p <.0001). Multivariate stepwise regression analysis showed that only the difference of daily given-recommended dietary allowances protein and the total repleted energy were positively correlated (r(2) =.47, p <.001 and r(2) = 34, p =.003, respectively) and multiple organ system failure negatively correlated with the NB (r(2) = -.24, p <.03) on the 5th day of the EEN protocol. Our data suggest that achievement of positive protein and energy balance in relation to the basic metabolic rate using an aggressive EEN protocol improves NB during the acute phase of stress in 2/3 of critically ill children.