This study was designed to compare and evaluate the effects of two isocaloric parenteral nutrition infusions, FreAmine and F080, differing in their amino acid composition, on the apparent nitrogen balance and urinary excretion of 3-methylhistidine in children with trauma (n = 27) or grave infection (n = 24). Trauma patients at the beginning of parenteral nutrition showed a more negative nitrogen balance than infected children, but in all children the apparent nitrogen balance increased to become positive and the 3-methylhistidine urinary excretion dropped. No differences related to the amino acid composition of the parenteral nutrition solutions were found. Apparent nitrogen balance and 3-methylhistidine excretion were correlated in all study groups irrespective of urine sample time. The enriched branched chain amino acid solution used for parenteral nutrition of trauma and infected children did not show a better effect than the non-enriched one in terms of muscle catabolism and nitrogen balance. The use of adequate nutritional support including both amino acids and energy source is of major importance in children recovering from trauma and infection.