Influenza A viruses are responsible for significant morbidity and mortality after bone marrow transplantation. Here we report failure of inhaled zanamivir treatment in a bone-marrow transplant recipient with pneumonia caused by an influenza A (H1N1) virus, although the influenza viruses isolated from bronchoalveolar lavages before and after treatment were clearly found to be sensitive to zanamivir using cell-based and enzymatic assays. Subsequent oral treatment with oseltamivir allowed complete recovery. Poor bioavailability of zanamivir in the peripheral lungs might have been limiting treatment efficacy in such an immunocompromised patient.