Background:We compared brain cortical and subcortical gray matter volumes and cortical thickness between postFontan patients and healthy controls, and examined brain anatomical associations with operative and medical history characteristics. Methods: Post-Fontan (n = 128 volumes; n = 115 thickness) and control subjects (n = 48 volumes; n = 45 thickness) underwent brain MRI at ages 10-19 y. Subcortical and cortical volumes and cortical thicknesses were measured for intergroup comparison. Associations between brain measures and clinical measures were assessed in the Fontan group. results: Widespread, significant reduction in brain volumes and thicknesses existed in the Fontan group compared to controls, spanning all brain lobes and subcortical gray matter. Fontan subjects treated with vs. without the Norwood procedure had smaller volumes in several terminal clusters, but did not differ in cortical thickness. Older age at first operation and increasing numbers of cardiac catheterizations, operative complications, and catheterization complications were associated with lower regional volumes and thicknesses. Increasing numbers of operative complications and cardiac catheterizations were associated with smaller regional volumes in the Norwood group. conclusion: The post-Fontan adolescent brain differs from the normal control brain. Some of these differences are associated with potentially modifiable clinical variables, suggesting that interventions might improve long-term neurocognitive outcome.c ongenital heart disease (CHD) is the most common congenital anomaly, with single ventricle (SV) defects occurring in nearly 10% of patients with CHD (1). Patients with SV, particularly hypoplastic left heart syndrome (HLHS), have higher mortality and morbidity than those with other types of CHD, but their survival has steadily increased for several decades (2). The Fontan procedure, as well as staged palliation