Measuring the volume and quantifying the shape of orbits is a technical challenge. Here we aimed to define methods for measuring orbital volume and characterising orbital shape in patients with FGFR2-related craniosynostosis. CT-scan data from 29 Crouzon and 15 Apert patients were assessed against age-matched controls. Orbital volume was computed using mesh-based semi-automatic haptic aided segmentation and by manual segmentation, with inter- and intra- observer control. Orbital shape was assessed using 23 reproducible 3D landmarks, 5 angles, and 8 distances, and by a registration-based comparison of mean orbital volume renderings. Volume measurement methods were reproducible. Control orbital volume rose from 14–21cc aged 2–10 yrs to a plateau of 22cc aged >10 yrs. Orbital volume was significantly reduced in CPS but not in AS. The orbital shape in CPS and AS was compressed in the anteroposterior axis and expanded anteriorly along the vertical axis. We describe reliable methods for measuring orbital volume and characterizing orbital shape. We show that FGFR2-related craniosynostoses affect the volume and the 3D shape of the orbits. Similar investigations on skulls with intentional deformations (Khonsari et al., Am J Phys Anthropol, 2013) provide insight on the comparative effects of external and internal constraints on craniofacial growth.