Atypical carcinoid tumors above the diaphragm are extremely rare and are associated with unfavorable clinical outcomes compared to typical carcinoid tumors. We described various clinical and histological features and investigated outcomes in patients with atypical carcinoid tumor of the lung and thymus. Medical records were reviewed in patients diagnosed with atypical carcinoid tumor of the lung or thymus at Samsung Medical Center between December 2003 and April 2010. We reviewed patient characteristics and treatment modalities and analyzed patient outcome in terms of disease-free survival and overall survival. Of the nineteen study patients, there were twelve patients with atypical carcinoid tumors of the lung and seven patients with thymic ones. All patients except one underwent complete resection as the main treatment. All patients who had tumors with lesser mitoses (≤5/10 high-power fields) are presently alive; moreover, they are all free of recurrence except for one patient who is also alive with recurrent tumor without any palliative treatment. Distant metastasis after curative resection developed in six patients and two of them died of progressive disease 25-31 months after recurrence even after palliative systemic chemotherapy. Atypical carcinoid tumor of the lung and thymus was a malignant disease that was prone to metastasize to distant sites even after curative resection and adjuvant treatment. Number of mitosis was a predicting factor for recurrence of disease and death in patients with atypical carcinoid tumor of the lung and thymus.