Chordomas and chondrosarcomas occur rarely in the skull base and have been often considered commonly with respect to the management. The aim of this study was to investigate the clinical results in each series of these tumors and analyze comparative outcome. Between 1991 and 2005, 30 consecutive patients with pathological diagnosis of chordoma (n=19) or chondrosarcoma (n=11) of the skull base were managed by multimodal treatment combining surgical resection with conventional photon radiotherapy and/or gamma knife radiosurgery. A retrospective analysis was conducted on these patients (aged 3 to 69 years; mean age of 37.3 years; 17 females and 13 males; mean follow-up of 56.1 months). Four deaths occurred among the patients with chordoma. The progression-free survival rate at 3 and 5 years was 61.5 and 40.0% in chordoma. In contrast, no mortalities were observed, and there was only one recurrence among the patients with chondrosarcoma. The progression-free survival rate at 3 and 5 years was 88.9 and 80.0% in chondrosarcoma. Among 15 survivors with chordoma, four patients were suffering from severe disability with progressive disease. On the other hand, most patients with chondrosarcoma harbored stable disease and less disabling symptoms except one instance of recurrence. As the biological behavior of chordoma is much more aggressive than that of chondrosarcoma in the skull base, one should make a distinction between these entities to plan an optimal treatment strategy.