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3-Methylglutaconic (3-MGC) aciduria with 3-methylglutaconyl-CoA hydratase deficiency (3-MGC aciduria type I) is a rare inherited metabolic disease of L-leucine catabolism. We describe a 9-month-old Japanese boy with this disorder who showed progressive neurological impairments presented as quadriplegia, athetoid movements and severe psychomotor retardation from 4 months of age. This finding indicates the existence of clinical heterogeneity in 3-MGC aciduria type I, suggesting it may present as a neurometabolic disease.