We investigated three-dimensional, depth-encoded line representations of neocortical sulci calculated from magnetic resonance image (MRI) datasets of 19 pairs of normal monozygotic twins. Monozygotic co-twins were significantly more alike than control pairs of unrelated twins matched from the same sample. Sulcal depth influenced sulcal similarity, with deeper sulci being more similar than superficial sulci. This was true both for the pairs of related co-twins and for the unrelated pairs, although the sulcal depth effect was stronger for the related twins. Our results indicate that the shape of deep (ontogenetically early) sulci of the human brain is more strongly predetermined than that of superficial sulci. The finding that sulcal similarity increased with sulcal depth especially within monozygotic twin pairs should stimulate further investigations of the relative importance of genetic versus shared environmental morphogenetic factors that must account for this result. In addition, we found that subjects with similar brain shape also have more similar sulcal patterns, suggesting that both features are the result of ontogenetically related processes. Sulcal comparisons across the entire sample suggested that the left posterior lateral hemispheric surface may be the least variable brain area. Methodologically, these results were obtained by the representation of sulci as three-dimensional polygonal lines (termed 'sulcal cuts') that are extracted automatically from MRI data sets using new image analysis techniques.