We present an autopsy case of the influenza virus A/H1N1 2009 pneumonia. A 58-year-old man, who is a resident of a nursing home, developed a fever above 38.0°C 3 days before admission, followed by an acute respiratory deficiency. He was transferred to our hospital, where the presence of pneumonia was confirmed by a chest radiograph. A rapid influenza diagnostic test was positive for influenza A, and he was immediately administered an anti-influenza drug and antibiotics. Nevertheless, the patient succumbed to pneumonia 3 days after hospitalization. His lung brush tissue was positive for influenza virus A/H1N1 2009 by real-time reverse transcription polymerase chain reaction (rRT-PCR) performed at autopsy. Histopathology of the lung tissue sections demonstrated diffuse alveolar damage with hyaline membrane formations. Immunohistochemical staining revealed influenza antigen-positive cells in the submucosal glands and pneumocytes. At the end of the 2010/2011 season, the Ministry of Health, Labor and Welfare recommended that the virus should be managed by the same measures the seasonal viruses were. However, several differences exist between the clinical characteristics that include the type of target cells and the ages of the at-risk patients. The validity of the Ministry's recommendation should be continued to be tested by careful clinical observations.