We present three patients with intrathoracic malignant neurogenic tumor. Two lesions showed no sign of invasion into adjacent structures, while the third lesion extended to the intraspinal canal with vertebral involvement. Although all three lesions were completely excised, each patient relapsed within 1 year of the initial treatment. One patient with local recurrence underwent radiation therapy, but the recurrent tumor continued to progress. Chemotherapy was subsequently performed. Two patients with distant metastases also received chemotherapy. Because there is no effective chemotherapeutic regimen for intrathoracic malignant neurogenic tumor, all three patients received high-dose chemotherapy followed by hematopoietic stem cell transplantation. Although the relapsed lesions temporarily regressed after treatment, all three patients showed disease recrudescence and ultimately died of their disease. A comparison of the intrathoracic malignant neurogenic tumors and the benign neurogenic tumors resected at our institution revealed no meaningful differences distinguishing malignant from benign neurogenic tumors prior to surgery.