This report presents the cases of two patients with rapidly progressive hypoxemia associated with influenza A(H3N2) virus infection, who were diagnosed with influenza related acute pulmonary microthromboembolism by serum D-dimer, lung perfusion and ventilation scans and computed-tomography scan of the chest, and were successfully treated by anti-coagulant therapy. The present cases suggest that acute onset pulmonary microthromboembolism should be considered in some patients with sudden, unexplained dyspnea during an outbreak of influenza infection and prompt diagnosis is essential to save the patient from acute death associated with influenza.