HSCT associated morbidity and mortality is usually attributed to high-dose chemotherapy/radiotherapy regimens used for conditioning. Glutamine (Gln), a conditionally essential amino acid during severe catabolic states, has been shown to have favorable effects in patients with malignancies and in those undergoing HSCT. However, controversy exists regarding its routine use. Studies in children investigating gln supplementation are very limited. In the present study, including 21 gln-supplemented and 20 control pediatric patients, gln supplementation was shown to reduce the duration of fever and decrease the incidence of SOS during the HSCT course. In addition, a decrease in drug-related toxicity and a trend toward reduced incidence of severe mucositis were observed.