Background: Cerebral structural changes related to obstructive sleep apnoea (OSA) have been reported in adult OSA patients; however, similar data and their associations with neurocognitive dysfunction are scarce in childhood OSA. Objective: To compare neurocognitive function, regional grey matter density and cerebral volume in children with and without OSA. Methods: Fifty OSA cases and 27 normal controls underwent a panel of neurocognitive tests. High resolution 3-dimensional magnetic resonance images of the brain were obtained from 23 OSA cases and 15 gender and age matched controls. Total cerebral volume and regional grey matter density were analyzed using voxel-based morphometry technique and compared between the two groups. Individuals with an obstructive apnoea hypopnoea index (OAHI) > 5 were defined as having moderate-to-severe OSA. Results: Children with OSA showed significantly reduced attention and visual-fine motor coordination scores compared with controls. Grey matter volume deficit was observed in prefrontal and temporal regions of cases with moderate-to-severe OSA only. Significant negative correlations were found between the visual-fine motor coordination score and the ratio of grey matter volume over total brain volume. Conclusion: Children with OSA had impaired attention and visual-fine motor coordination. Regional grey matter reduction was evident in children with more severe OSA.