Patients with advanced interstitial lung disease are at an increased risk of developing primary pulmonary malignancies. Although some literature exists concerning the development of malignancy after lung transplantation, less is known regarding the detection, management, and clinical outcome of unexpected pulmonary malignancy discovered by explant examination. We present a case of a 51-year-old man with a prolonged history of diffuse parenchymal lung disease classified as bronchiolitis obliterans organizing pneumonia and chronic interstitial pneumonia. Although the patient never developed myositis, serologic studies at diagnosis revealed the presence of an anti-Jo1 antibody. Nineteen years after diagnosis, the patient underwent bilateral lung transplantation. Pathological evaluation of the explanted lungs revealed unexpected invasive mucinous adenocarcinoma diffusely involving both lungs and all lobes, with metastatic adenocarcinoma involving hilar lymph nodes and soft tissue. Of note, the patient had a history of recurrent thromboembolic phenomenon previously well-managed with warfarin. Six months before transplantation, the patient developed warfarin-resistant thromboembolic disease requiring low–molecular weight heparin therapy. Although cases of unexpected explant pulmonary malignancy are uncommon, they raise challenging questions regarding the management and prognosis of such patients. Because of the alterations in the background lung parenchyma, detection of underlying malignancy in these patients is difficult for both the radiologist and the pathologist. Factors related to pretransplant screening for malignancy are reviewed. The development of heparin-responsive thromboembolic disease in a patient previously well-managed with warfarin is discussed as a clinical clue to underlying malignancy in this patient.