Rare neoplastic diseases including sarcomas can occur in the middle mediastinum. Obtaining a histological specimen is crucial for diagnosis and for establishing a treatment plan. Our research group has recently reported a minimal invasive method of tissue sampling of the mediastinum using direct real-time endobronchial ultrasound-guided transbronchial needle aspiration. By the use of this new modality, histological cores can be obtained for pathological diagnosis that can be used for immunohistochemistry as well as genetic analysis. A very rare case of spinal chondrosarcoma due to hereditary multiple exostoses successfully diagnosed by endobronchial ultrasound-guided transbronchial needle aspiration and by immunohistochemistry with genetic analysis is reported.