The clinical, 18fluorodeoxyglucose positron emission tomography (18FDG PET) and the magnetic resonance imaging (MRI) brain scan characteristics of four patients diagnosed to have 3-methylglutaconic aciduria were reviewed retrospectively. The disease has a characteristic clinical pattern. The initial presentations were developmental delay, hypotonia, and severe failure to thrive. Later, progressive encephalopathy with rigidity and quadriparesis were observed, followed by severe dystonia and choreoathetosis. Finally, the patients became severely demented and bedridden. The 18FDG PET scans showed progressive disease, explaining the neurological status. It could be classified into three stages. Stage I: absent 18FDG uptake in the heads of the caudate, mild decreased thalamic and cerebellar metabolism. Stage II: absent uptake in the anterior half and posterior quarter of the putamina, mild-moderate decreased uptake in the cerebral cortex more prominently in the parieto-temporal lobes. Progressive decreased thalamic and cerebellar uptake. Stage III: absent uptake in the putamina and severe decreased cortical uptake consistent with brain atrophy and further decrease uptake in the cerebellum. The presence of both structural and functional changes in the brain, demonstrated by the combined use of MRI and 18FDG PET scan, with good clinical correlation, make the two techniques complementary in the imaging evaluation of 3-methylglutaconic aciduria.