We describe the findings on single photon emission computed tomography (SPECT) in a patient who had genetically definite megalencephalic leukoencephalopathy with subcortical cysts. Technetium-99m-ethyl cysteinate dimer SPECT revealed hypoperfusion in the cerebral white matter, which had shown high signal intensity on magnetic resonance imaging (MRI) T2 images. Hypoperfusion was also unexpectedly found in the frontal cortices, which showed no abnormalities on MRI. This frontal abnormality corresponded clinically to a low score on the frontal assessment battery. Decreased GABA receptor density as suggested by (123)I-Iomazenil SPECT provided further evidence of cortical neuron dysfunction. Although confirmation must await future larger-scale SPECT and functional studies, our findings suggest that SPECT can be used to non-invasively monitor in vivo cortical function in this disease.