BACKGROUND: Palliative procedures performed before the Fontan procedure may require ligation of the subclavian arteries, thereby affecting flow to the vertebral arteries. In adults with functionally univentricular heart disease, the implications of altered brainstem vascular anatomy for perioperative management of failing Fontan circulation are not known. METHODS: We identified abnormal posterior circulation anatomy in an adult patient with failing Fontan circulation who experienced a brainstem stroke after Fontan conversion. We then changed our clinical practice to include detailed preoperative neurologic evaluation of adults with univentricular heart disease and failing Fontan circulation. Here, we report the clinical and neuroimaging findings in 5 consecutive patients before and after this change in practice. RESULTS: Five patients ages 28 to 42 years had Fontan procedures performed in childhood, and underwent either Fontan conversion or cardiac transplantation. Patient 1 experienced an episode of decreased cerebral perfusion pressure on postoperative day 3, and experienced an ischemic brainstem stroke causing transient locked-in syndrome. A change in practice was made, and patients 2, 3, and 4 were evaluated preoperatively by the neurocritical care service. These patients then had higher target blood pressures perioperatively and no neurologic injury. Patient 5 was evaluated for symptoms consistent with subclavian steal. Neuroimaging in 3 patients was abnormal, with atrophic vertebral arteries, an occluded vertebral artery, and retrograde perfusion of a vertebral artery. CONCLUSIONS: In adults with failing Fontan circulation there is a potential for neurologic complications as a result of venous congestion with elevated central venous pressures, and aberrant posterior circulation. The patient's history and brain imaging may be used to identify at-risk patients and to tailor perioperative management during Fontan conversion or heart transplantation to mitigate the risk for brainstem ischemia.