Upon 273 days after starting imatinib mesylate therapy, a 73-year-old woman with gastrointestinal stromal tumor without any symptoms presented with an abnormality on computed tomography. The abnormality, which was a consolidation in the peribronchovascular bundle, progressively developed after she discontinued imatinib mesylate. She presented with progressive cough and dyspnea. A histopathological examination of the surgical lung biopsy specimen revealed polypoid plugs of organizing connective tissue within the alveolar spaces and lymphocytic infiltration into the alveolar wall. She was therefore diagnosed as having imatinib mesylate-induced organizing pneumonia. She was treated by corticosteroid therapy. Her symptoms improved and the consolidation in the peribronchovascular bundle was resolved. Imatinib mesylate-induced lung disease presents as various abnormalities. The progression of pneumonitis rarely occurs in patients after discontinuing imatinib mesylate treatment. The histopathological analysis of the surgical lung biopsy was useful for definitive diagnosis and predicting the prognosis and treatment response in this patient.