We reviewed the results of 68 consecutive Fontan procedures from 1978 to 1993 to determine the frequency of late central neurologic complications of the Fontan procedure in patients living at a mean altitude of 4500 feet. Two surviving patients had transient neurologic symptoms or signs with no corresponding evidence of brain injury by magnetic resonance imaging (MRI), whereas six surviving patients had strokes defined by sustained neurologic symptoms or signs with areas of brain injury identified by MRI [8.8% (6.0-13.0%; 70% confidence limits)]. Collectively, patients with neurologic symptoms had normal hemoglobin values, platelet counts, partial thromboplastin times, and prothrombin times at the onset of clinical neurologic findings. Two patients were taking antiplatelet agents, and one patient was taking warfarin. One of the patients with transient neurologic findings and all of the stroke patients had residual right-to-left shunts. Thus strokes were not uncommon in our patients after the Fontan procedure. Brain injury may result from thromboembolic events associated with residual right-to-left shunts, but our total number of asymptomatic patients with a residual shunt or brain abnormalities by MRI is not known.