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Granulomatosis with polyangiitis (GPA) can involve the skull base or the Eustachian tubes. GPA is diagnosed on the basis of clinical manifestations and serological tests, although it is challenging to discriminate GPA from infectious processes driving skull base osteomyelitis (SBO) and malignant processes such as nasopharyngeal carcinoma (NPC). Moreover, current serological tests have a low sensitivity and cannot distinguish GPA from these other conditions. We hypothesized that certain MRI characteristics would differ significantly among conditions and aimed to evaluate whether the features could differentiate between GPA, SBO, and NPC involving the skull base. We retrospectively evaluated the MRI findings of patients with GPA, SBO, and NPC. We performed univariable logistic regression analyses to identify the predictive variables for differentiating between conditions and evaluated their diagnostic values. We showed, for the first time, that certain MRI findings significantly differed between patients with GPA and those with SBO or NPC, including the lesion morphology and extent, the apparent diffusion coefficient (ADC) values, the contrast enhancement patterns, the presence or absence of necrosis, and retropharyngeal lymphadenopathy. In conclusion, utilizing certain MRI features can improve the diagnostic performance of MRI by differentiating GPA with skull base involvement from other conditions with similar radiologic findings, including SBO and NPC, facilitating treatment plans and, thus, improving patient outcomes.