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Chordomas are rare tumors of the central nervous system and primarily occur in the extradural space. We report two patients with intracranial chordomas located in the region of the clivus that invaded the prepontine cisterns. The patients, 45 and 62 years old, had histories of cranial neuropathies and headache, respectively. Petrosal approaches were performed in both with radical resection of the tumors. Anatomopathological studies confirmed the diagnosis of chordoma. The symptoms of both patients resolved, and they have had no recurrence after 18 months of follow-up. Intradural chordomas or extradural chordomas that invade the intradural space are difficult to differentiate from ecchordoses physaliphorae, a non-neoplastic entity with similar radiological features. MBI-1 studies were therefore performed to confirm the diagnosis of chordoma. The differential diagnosis for these two entities, the different modalities of treatment, and prognosis are reviewed.