This study aimed to investigate the incidence of direct invasion and metastasis of nasopharyngeal carcinoma (NPC) at different anatomic sites in the skull base using magnetic resonance imaging (MRI). MRI data from 101 NPC patients with skull base invasion were collected and we analyzed the incidence and anatomic sites of invasion of NPC in the skull base. Of the 101 NPC patients, 84 had direct invasion at the skull base (83.2%), and 17 had skull base metastasis (16.8%). Affected sites with direct invasion in the skull base included sphenoid sinus and sella base, cavernous sinus, internal carotid canal, and clivus blumenbachii. Skull base metastasis sites included the internal carotid canal and jugular foramen area. Because of early lymphatic metastasis of NPC to the skull base, MRI examination can be helpful in increasing the accuracy of diagnostic imaging for skull base invasion of NPC and selecting appropriate target sites, radiotherapy techniques, and operative approaches. Anat Rec, 2012. (C) 2012 Wiley Periodicals, Inc.