Background: Velocardiofacial Syndrome (VCFS) is the most common human genetic deletion syndrome and young people with VCFS are at substantial risk for developing psychosis in later life. It has been reported that people with VCFS have significant differences in white matter volume. However, there are few in vivo studies of white matter microstructural integrity (as measured using Diffusion Tensor (DT)‐MRI), and nobody has related differences in white matter anatomy to schizotypy in VCFS children or adolescents. Method: We used (respectively) DT‐MRI and voxel based morphometry (VBM) to measure the fractional anisotropy (FA) and proportion of white matter in 11 VCFS children and adolescents and 12 controls (7 of whom were siblings). Also, within people with VCFS we carried out a preliminary analysis in which we related differences in white matter to severity of schizotypy. Results: VCFS, compared to controls, had a significantly lower FA in frontal, parietal and temporal lobe regions as measured using DT‐MRI. In contrast, FA was significantly higher than controls in the internal capsule, anterior/superior corona radiata and corpus callosum. Using VBM we found a significantly smaller proportion of white matter in the cerebellum, occipital lobes and hippocampus but a significantly higher amount in the internal capsule, basal ganglia, cingulum and corpus callosum in VCFS. Also, within people with VCFS, FA of the internal capsule was significantly positively correlated with severity of schizotypy. Conclusion: Young people with VCFS have significant differences in white matter microstructure and volume. Some, but not all of these, overlap with each other. Also, within VCFS, regional differences in FA are associated with schizotypal behaviour.