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5-HT3 receptor antagonists, including granisetron and ondansetron, are widely used in the prophylactic treatment of chemotherapy-induced nausea and vomiting. Although the cardiac safety of granisetron and ondansetron has been investigated in several adult studies, there is no report investigating the effects of those agents on electrocardiography (ECG) in children. The effects of intravenously infused (over 30 seconds) 0.1 mg/kg ondansetron and 40 μg/kg granisetron on ECG were assessed in 22 children receiving high-dose methotrexate therapy for acute lymphoblastic leukemia. The ECG recording was obtained at before and just after the infusion, and repeated at 1, 3, 6, and 24 hours of treatment. Granisetron administration resulted in a statistically significant decrease of mean heart rate at 1 and 3 hours, and significant prolongation of mean QT and QTc dispersions at 1 hour of infusion. In patients treated with ondansetron, no meaningful change was observed. In conclusion, intravenous granisetron but not ondansetron causes clinically asymptomatic and transient changes on ECG measurements in children receiving high-dose methotrexate therapy.