After a 17-year-old woman with ulcerative colitis was treated with granulocyte apheresis, chest imaging showed multiple nodular infiltrates, including one which seemed to have a cavity. Wegener's granulomatosis was suspected because proteinase-3 anti-neutrophil cytoplasmic antibody levels were increased. Transbronchial lung biopsy specimen showed nonspecific findings. Chest imaging showed clearing of pulmonary infiltrates without any therapy or discontinuation of mesalazine, which is known to cause lung toxicity. To the best of our knowledge, this is the first report of extra-intestinal pulmonary complications of ulcerative colitis with elevated proteinase-3 anti-neutrophil cytoplasmic antibody resembling Wegener's granulomatosis and spontaneous improvement.