Alexander disease is a progressive neurodegenerative disease, which can present with brainstem lesions with imaging characteristics similar to multifocal low-grade glioma, thus presenting a diagnostic dilemma. The authors report a 6-year-old child presenting with multifocal brainstem lesions subsequently diagnosed to have Alexander disease. In vivo magnetic resonance spectroscopy generated a metabolite profile of the lesion allowing differentiation from low-grade glioma. Magnetic resonance spectroscopy is a powerful tool in the assessment of brainstem lesions and is a useful adjunct to conventional magnetic resonance imaging in the assessment and diagnosis of atypical brain lesions.