After influenza vaccination an 83-year-old woman was referred to us because of fever and sore throat with no response to antibiotics. Chest computed tomography showed thickened bronchovascular bundles, multiple nodules with feeding vessels, and consolidation. Laboratory tests showed a high level of serum myeloperoxidase anti-neutrophil cytoplasmic antibody (MPO-ANCA) and soluble interleukin-2 receptor (sIL-2R), as well as abnormal renal function and urinary sediment. Transbronchial lung biopsy revealed organizing pneumonia. We made a diagnosis of microscopic polyangiitis after influenza vaccination. Corticosteroids and cyclophosphamide were effective. Careful attention should be paid to severe adverse effects such as systemic vasculitides after influenza vaccination.