We reported a 28-year-old man with multiple lesions in the brainstem which were clearly identified and followed up with MRI. He had been treated for Behçet uveitis using cyclosporine and colchicine during the past 5 years, and he acutely presented with fever and headache, followed left hemiparesis, dysarthria and dysphagia. MRI on admission revealed multiple lesions in the ventral pontine region which showed mixed-intensity on T1WI, high-intensity on T2WI and enhancement with Gd-DTPA. His clinical symptoms spontaneously and gradually improved, but more rapidly improved due to additional administration of corticosteroid. The lesions in the brainstem became smaller and finally rudimentary during two months after the onset of neurological symptoms.