A low plasma glutamine concentration (<420 µmol/L) is an independent risk factor for mortality in critically ill adult patients. Glutamine metabolism in children is less well characterized. However, pediatric ICU (PICU) mortality is low and, therefore, mortality is difficult to use as an endpoint. Here we evaluated if plasma glutamine concentration at admission to the PICU, relates to the development of multiple organ failure, using pediatric logistic organ dysfunction score (PELOD)-score. In this observational study, consecutive critically ill children (n = 149) admitted to the PICU of a tertiary university hospital as well as a reference group of healthy children (n = 60) were included. Plasma glutamine concentration and the PELOD were determined at admission for all patients and at day 5 for those patients still in the PICU. Plasma glutamine concentration at admission was low in the PICU patients as compared to controls (p = 0.00002) and patients with a low plasma glutamine concentration had more organ failure as compared to patients with higher plasma glutamine concentration (p = 0.0001). Plasma glutamine concentration normalized in patients staying >5 days in the PICU. Plasma glutamine depletion was present in 40 % of patients at PICU admission and it was associated with the development of multiple organ failure. Furthermore, the majority of the critically ill children normalized their plasma glutamine concentration within 5 days, which is different from adult ICU patients. The study suggests that an initial plasma glutamine deficiency is associated with multiple organ failure in critically ill children.