Megalencephalic leukoencephalopathy (MLC) with subcortical cysts is an infantile-onset inherited disease of the brain white matter with a defect in brain ion and water homoeostasis, which leads to an abnormal brain volume regulation. Clinical features of the disease can be variable, but patients typically show early-onset macrocephaly, motor abnormalities, seizures, and almost constant late-onset mild mental deterioration. Brain magnetic resonance imaging (MRI) reveals diffusely abnormal and mildly swollen white matter as well as subcortical cysts in the anterior temporal and frontoparietal regions. We describe here clinical findings and volumetric MRI and (1)H-MR spectroscopic imaging ((1)H-MRSI) data of a 12-year follow-up on a patient with MLC. The patient had only slight clinical worsening during the long follow-up. Volumetric findings showed substantially unchanged cystic volumes and mild brain atrophy rate. In addition, there was no over time increase in the volume of white matter hypointense lesions seen on FLAIR images at baseline, but the degree of hypointensity of these white matter voxels increased over 12 years. Longitudinal (1)H-MRSI examination showed long-term undetectable metabolite signals in the white matter, whereas the metabolic pattern of gray matter voxels remained unchanged over time. Results show that, in MLC, the chronic brain white matter changes resulting from the brain ion, and water homeostasis can be monitored by quantitative MRI modalities. This might be important for assessing treatment effects.