Megalencephalic leukoencephalopathy with subcortical cysts (MLC) is a recently recognized neurological disease, and mutations in the MLC1 gene have been identified as the cause of the disorder. A 54-year-old Japanese woman with macrocephaly presented with progressive mental decline, gait disturbance due to spasticity and ataxia, and choreoathetotic movement in the left upper extremity. Brain magnetic resonance imaging (MRI) revealed characteristic subcortical cysts in addition to diffuse white matter involvement. Genetic analysis of the MLC1 gene identified an S93L mutation in a homozygous state. This case is particularly valuable because of the lack of knowledge on the long-term prognosis of MLC.