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To compare white matter microstructure in children and adolescents with single ventricle who underwent the Fontan procedure with healthy controls, and to explore the association of white matter injury with cognitive performance as well as patient and medical factors.Fontan (n = 102) and control subjects (n = 47) underwent diffusion tensor imaging (DTI) at ages 10-19 years. Mean DTI measures (fractional anisotropy, radial diffusivity, axial diffusivity, and mean diffusivity) were calculated for 33 fiber tracts from standard white matter atlases. Voxel-wise group differences in DTI measures were assessed using Tract-Based Spatial Statistics. Associations of regional fractional anisotropy with IQ and processing speed as well as medical characteristics were examined.Subjects with Fontan, compared with controls, had reduced bilateral regional and voxel-wise fractional anisotropy in multiple white matter tracts along with increased regional radial diffusivity in several overlapping tracts; regional mean diffusivity differed in 2 tracts. The groups did not differ in voxel-wise radial diffusivity or mean diffusivity. Among subjects with Fontan, fractional anisotropy in many tracts correlated positively with Full-Scale Intelligence Quotient and processing speed, although similar findings were absent in controls. Lower mean fractional anisotropy in various tracts was associated with more complications in the first operation, a greater number of total operations, and history of neurologic event.Children and adolescents who have undergone the Fontan procedure have widespread abnormalities in white matter microstructure. Furthermore, white matter microstructure in several tracts is associated with cognitive performance and operative and medical history characteristics.