Apert syndrome is characterized by hypertelorism, a negative canthal axis, and central midfacial hypoplasia, resulting in a biconcave face. Bipartition distraction partially corrects these facial anomalies. This study investigates limitations of bipartition distraction using linear, angular, and geometric morphometric analysis. Preoperative and postoperative three-dimensional computed tomographic craniofacial constructs of 10 patients with Apert syndrome (aged 12 to 21 years) were annotated with 98 landmarks. Twelve age-, sex, and ethnicity-matched normal skulls provided control data. Principal component analysis was used to analyze shape characteristics within and between the groups and describe the changes occurring with surgery. Results were displayed graphically using difference color maps. Conventional point-based measurements documented midfacial width, height, and asymmetry. Apert three-dimensional constructs exhibited reduced upper midfacial height and greater extrinsic symmetric variation relative to controls. Facial bipartition partially corrected excessive midfacial width and interorbital distance but did not adequately correct deficient upper midfacial height. Excessive orbital diameter was unaltered by surgery. There was no demonstrable effect on intrinsic or extrinsic midfacial asymmetry. Principal component analysis demonstrated improved midfacial projection and correction of central biconcavity. Bipartition distraction corrects midfacial retrusion, exorbitism, and hypertelorism. It does not treat midfacial height disproportion or correct orbital shape. It leaves the face too wide at the zygomatic level and does not correct facial asymmetry. Although bipartition distraction is an improvement on the unmodified monobloc advancement, further refinements are needed to fully correct Apert dysmorphology.