Following surgical management of craniosynostosis, residual calvarial defects may require reconstruction, frequently with the use of cranial bone grafts. Knowledge of optimal sites for harvest would be beneficial in such situations. The goal of this study is to compare calvarial thickness (CALV) and diploic thickness (DIPL) in children with corrected sagittal synostosis to normal controls (n = 47) using postoperative CT scans. We also compare the results from children who had undergone open (OPEN) (n = 26) and endoscopic (ENDO) (n = 26) surgery. On each skull, CALV and DIPL were measured at 44 points over 5 regions. Multiple regression analysis was used to compare CALV and DIPL controlling for gender and age. Children who had undergone previous craniosynostosis correction tended to have thinner CALV compared to controls in operated regions but thicker CALV in unoperated regions (P < 0.001). Adjusted mean CALV was thinner overall in ENDO compared to OPEN (P = 0.020). Children with corrected sagittal synostosis have thinner DIPL than controls (P = 0.002). No difference was found in DIPL comparing OPEN and ENDO (P = 0.977) approaches. Children who had undergone previous craniosynostosis correction tended to have thinner CALV when compared to controls in operated regions but thicker CALV in unoperated regions. ENDO calvaria were thinner than OPEN calvaria. Children with corrected sagittal synostosis have thinner DIPL than controls; no difference was found in DIPL comparing OPEN and ENDO approaches. Due to irregularities in bone development among children who had previously undergone calvarial reconstruction, individualized preoperative CT assessment is recommended in all patients undergoing secondary split calvarial bone grafting procedures.