Eleven children who had post-pump choreoathetosis develop after cardiopulmonary bypass were evaluated in their perioperative course to determine factors that may correlate with their neurologic outcome. Results showed that preoperative cyanosis is associated with the development of a basal ganglia lesion. An acquired basal ganglia lesion and preoperative cyanosis are associated with persistence of post-pump choreoathetosis. The combination of cyanotic heart disease and a scan-identified basal ganglia lesion indicates a poor prognosis for the patient with persistent post-pump choreoathetosis. Also, the presence of total circulatory arrest is associated with a decrease in developmental quotient but not the persistence of post-pump choreoathetosis.