Background. It is known that the sensitivity of rapid tests using a nasopharyngeal swab is low in cases with influenza H1N1 and definitive diagnosis is difficult in some cases. Case. A 33-year-old man complained of fever and cough, and received a rapid influenza test using a nasal swab at a nearby clinic in February 2011, which was negative. Since dyspnea appeared and a chest X-ray film showed ground-glass shadows in both lungs, he was referred to our clinic. Although 4 rapid nasopharyngeal swab tests were negative and reverse transcription polymerase chain reaction (RT-PCR) for influenza A (H1N1) using a nasal swab also was negative, RT-PCR using bronchoalveolar lavage fluid (BALF) was positive and influenza (H1N1) was diagnosed. He developed severe pneumonia complicated with acute respiratory distress syndrome (ARDS), but daily repeated infusion of peramivir ameliorated it. Conclusion. Sample collection from the lower airway and RT-PCR were useful for definitive diagnosis in this case. Further accumulation of such cases is needed to show the efficacy of repeated infusion of peramivir.