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Progressive multifocal leukoencephalopathy (PML) is a severe infection caused by the polyomavirus JC that develops in the central nervous system (CNS) of immunosuppressed patients. The infection frequently starts in the brain hemispheres and can spread into other CNS regions such as the brainstem. Initial isolated PML brainstem lesions are exceptional. We aimed to describe the challenging diagnosis of PML with isolated brainstem lesions at the time of disease onset. We describe a case of PML starting with an isolated brainstem lesion and