We report three patients with non-germinomatous malignant germ cell tumor (NGMGCT) who developed therapy-associated secondary tumors. They were diagnosed as having NGMGCT by elevated serum levels of α-fetoprotein (AFP), human chorionic gonadotropin (HCG), or β-HCG. Preoperatively, all patients received a combination of etoposide and platinum-based chemotherapy and radiotherapy; neo-adjuvant therapy (NAT) was followed by complete excision of the residual tumor. Postoperatively, all underwent maintenance chemotherapy and all remained free of NGMGCT without recurrence. However, they developed therapy-associated secondary tumors, i.e. glioblastoma, meningioma, or cavernous angioma after 10.1, 9.8, and 8.2 years, respectively. The patient with glioblastoma died one year after its detection. The other two patients are currently alive; the meningioma was completely removed and the cavernous angioma is being monitored without additional treatment. To the best of our knowledge, therapy-associated secondary tumors in patients treated for NGMGCT are rare.