Objective Patients with craniocervical junction malformations (CCJM) tend to suffer more frequently from sleep respiratory disturbances, which are more frequent and severe in patients with basilar invagination. Here we evaluate if patients with CCJM and sleep respiratory disorders (SRD) present smaller airway dimensions than patients without SRD. Method Patients with CCCM with and without sleep respiratory disturbances were evaluated clinically by Bindal's score, modified Mallampati classification, full-night polysomnography and upper airway cone beam tomography. Results Eleven patients had sleep respiratory disorders (SRD), and nine patients performed control group without SRD. CCJM patients with SRD were predominantly female, older, had higher BMI, were more likely to have Mallampati grades 3 and 4 and had statistically significant smaller anteroposterior diameter of the upper airway than patients without SRD. Conclusion Patients with CCJM and sleep respiratory disturbances have higher BMI, higher Mallampati score and smaller anterior posterior diameter of the upper airway.