The overall volume of the brain has been found to be under relatively strong genetic control, but the relative strength of genetic and environmental factors on between-person variations in regional cortical thickness in adolescence is still not well understood. Here, we analyzed structural MRI data from 108 14-year-old healthy twins (54 females/54 males) to determine the relative contributions of genes and the environment toward regional variations in gray matter thickness across the cortex. After extracting cortical thickness values at a high spatial resolution, an A/C/E structural equation model that divides the variations into additive genetic (A), shared (C), and unique (E) environmental components was fitted. There was considerable regional variability in the magnitude of genetic influences on cortical thickness after controlling for sex. Regions with genetic contributions of greater than 80% were observed in the prefrontal cortex, predominantly in the bilateral dorsolateral and mesial superior frontal regions. No region showed prominent shared environmental influences, but unique environmental influences of over 80% were found in parietal association regions. The genetic variance for cortical thickness in adolescents in prefrontal regions overlapped with previous findings in adults. However, the unique environmental effects observed in multimodal parietal association cortices with converging inputs from visual, auditory, somatosensory regions, and neighboring secondary association cortices suggest that these regional variations are more shaped by experience and could form targets for early interventions in youth with behavioral disorders.