Megalencephalic leukoencephalopathy with subcortical cysts (MLC) is an autosomal recessive neurological disorder manifesting early onset macrocephaly and delayed-onset neurological deterioration. Characteristic radiological findings revealed by brain magnetic resonance imaging are the most important factors for obtaining a clinical diagnosis. In this study, we analyzed the causative gene, MLC1, in seven unrelated Japanese patients. The most common mutation in our study was p.S93L; this mutation was observed in 11 alleles (78.6%). The second most common mutation, p.A275D, was observed in two alleles (14.3%). A novel single-nucleotide deletion, c.578delG (p.V194Sfs*2), was identified in one allele. As the clinical severities of patients with MLC were variable even among those sharing identical genotypes, this condition may be modified by environmental factors, modifier genes or epigenetic factors.