Neuroimaging methods represent a critical tool in efforts to join the study of the neurobiology of genes with the neurobiology of behaviour, and to understand the neurodevelopmental pathways that give rise to cognitive and behavioural impairments. This article reviews the clinical features and highlights studies with a focus on the relevant gene-brain-behaviour connections observed in neurogenetic syndromes, such as Williams, Rett, Fragile X, Prader-Willi, Angelman, Down and velocardiofacial (22q11.2 deletion) syndromes. The relationship of altered brain regions and activation patterns are discussed for each syndrome, as well as the clinical, cognitive and behavioural correlates of these neuroimaging findings.