Since almost two decades, a considerable amount of work has been devoted to the accurate delineation of normal and abnormal brain development, using cerebral MRI. In the broad field of neuroimaging research, specific genetic conditions associated with impaired cognitive performances or with psychiatric symptoms have received increased attention, due to their potential for revealing insight on the biological correlates of behavior. First delineated by volumetric measurements of cerebral lobes or regions of interest, new image processing techniques are now defining cerebral phenotypes associated with neurogenetic disorders with increasing precision. We review here the contribution of structural brain imaging in advancing our understanding of the pathogenic processes underlying altered brain development in Down, Fragile X and Velo-cardio-facial (22q11DS) syndromes.