The ideal material for primary reconstruction of skull defect would be the autogenous bone. However, the long-term evaluation regarding the change in bone graft thickness has not been reported. In this article, we analyzed the thickness changes of the graft according to the time period. Between March 2005 and February 2011, a total of 29 patients underwent skull reconstruction with autogenous split calvarial bone grafts. After applying exclusion criteria, computed tomographic (CT) images of 15 patients were analyzed. The donor bone was harvested in full thickness as 1 piece and then as split. One half of the bone plate was transferred to the defect site; the other half, to the donor site. Both halves were fixed with titanium plates. To compare graft thickness changes, immediate postoperative and follow-up CT scans were analyzed by a single researcher. An anatomic reference was appointed for each patient, and the thickness of the graft on the same level was measured on time-series CT images. Collected data were analyzed with a polynomial random coefficient model. The main causes of the skull defects were trauma and tumor excision. In all cases, the graft thickness was not decreased but even increased in both the donor and recipient sites. The mean graft thicknesses between 6 months and 1 year after the surgery as well as those between 2 and 3 years after the surgery were 1.24-times and 1.56-times thicker than the immediate postoperative thickness, respectively. Graft thickness turned out to be either maintained or increased over time.