Structural magnetic resonance imaging (MRI) studies have started to address the contributions of genetic and environmental factors to brain morphology in healthy individuals. These studies have largely been limited to assessing heritability for single and mostly gross anatomical structures. To avoid this limitation, we developed a method using high-dimensional 3D nonlinear registration to apply an elastic deformation vector field in the cortical parameter space and assess regional cortical gray matter density on the entire cortical surface in healthy monozygotic (MZ) and dizygotic (DZ) twins. Once aligned across subjects, surface maps of gray matter density were subjected to variance component analyses. By fitting structural equation models, we generated cortical surface maps to reflect the regional percent variance explained by genetic, shared and unique environmental factors. Initial analyses suggest that cortical structure in primary motor and sensory areas is highly heritable with variance components for additive genetic influences reaching as high as 70%. ©2004 IEEE.