Purpose: This study was performed to compare the clinical characteristics of 2009 pandemic influenza A(H1N1) [A(H1N1) pdm09] and seasonal influenza A infection in the pediatric cancer patients. Methods: A retrospective review was performed in the pediatric cancer patients who had confirmed A(H1N1)pdm09 infection at Samsung Medical Center from August 2009 to February 2010. For the comparison, the medical records of pediatric cancer patients with seasonal influenza A from January 2000 to May 2009 were reviewed retrospectively. Results: Eighty-two A(H1N1)pdm09 infections were confirmed in the pediatric cancer patients. Ten patients (12.2%) developed complicated clinical course by lower respiratory infections or extrapulmonary infections; 4 pneumonia, 1 bronchitis, 1 pericarditis with pneumonia, 1 encephalitis with pneumonia, 2 meningitis and 1 pericarditis. Three patients received mechanical ventilator and ICU care. Three pediatric cancer patients (3.7%) died. The risk factors related to complicated A(H1N1)pdm09 infections were date of infection (44-45th week 2009) and nosocomial infection. When comparing with previous seasonal influenza A infections, more prompt and aggressive antiviral therapy was given in A(H1N1)pdm09 infections. Conclusion: The A(H1N1)pdm09 infections caused a various clinical manifestations including fatal cases in pediatric cancer patient during pandemic season. There was no significant difference in clinical course between influenza A(H1N1)pdm09 and seasonal influenza A infections except the antiviral treatment strategy.