Despite the clinical and pathologic indicators implicating injury to the basal ganglia in children with hyperkinetic movement disorders, we were previously unable to identify lesions in these structures by means of cranial computed tomography or magnetic resonance imaging. We evaluated regional cerebral perfusion measured by single photon emission computed tomography (SPECT) with technetium 99m hexamethyl propylene amine oxime as a technique to localize functional cerebral abnormalities in eleven children who had a movement disorder after hypothermic cardiac surgery. Perfusion defects of the deep gray matter were noted in six of these eleven patients and cortical perfusion defects in nine. For both cortical and subcortical defects a strong right-sided predilection was present. Our findings suggest functional brain injury not detectable by conventional cranial computed tomography and magnetic resonance imaging in these patients. We speculate that these perfusion defects might relate to the behavioral and developmental sequelae in survivors of this syndrome. SPECT may identify subclinical injury in patients at risk for future neurodevelopmental problems and contribute to our understanding of the mechanisms of cerebral injury in the patient operated on for cardiac disease.