Object: Craniosynostosis syndromes are characterized by prematurely fused skull sutures, however, less is known about skull base synchondroses. This study evaluates how foramen magnum (FM) size, and closure of its intra-occipital synchondroses (IOS) differ between patients with different craniosynostosis syndromes and control subjects; and whether this correlates to ventriculomegaly and/or Chiari malformation type I (CMI), intracranial disturbances often described in these patients. Methods: Surface area and anterior-posterior (A-P) diameter were measured in 175 3D-CT scans of 113 craniosynostosis patients, and in 53 controls (0-10 years old). Scans were aligned in a 3D multiplane-platform. The frontal and occipital horn ratio was used as an indicator of ventricular volume, and the occurrence of CMI was recorded. Synchondroses were studied in scans with a slice thickness <= 1.25 mm. A generalized linear mixed model and a repeated measures ordinal logistic regression model were used to study differences. Results: At birth, patients with craniosynostosis syndromes have a smaller FM than controls (p < 0.05). This is not related to the presence of CMI (p = 0.36). In Crouzon Pfeiffer patients the anterior and posterior IOS fused prematurely (p < 0.01), and in Apert patients only the posterior IOS fused prematurely (p = 0.028). Conclusion: The FM is smaller in patients with craniosynostosis syndromes than in controls, and is already smaller at birth. In addition to the timing of IOS closure, other factors may influence FM size. (C) 2015 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.