Neurodevelopmental disorders are thought of as beginning before birth, and many such as Down syndrome clearly do. Clinically, however, other such disorders may unfold over months (Mental Retardation, Autism, Rett syndrome) or years (Asperger Syndrome, Fragile X, Dyslexia). While structural Magnetic Resonance Imaging (MRI) has uncovered specific regions of white and gray matter abnormalities associated with several of these disorders, the exact relationship between structural changes and alterations in neuronal function and connectivity are still unclear. Over the past decade, functional brain imaging methods such as PET and SPECT have gained widespread clinical acceptance in other medical fields such as Oncology and Psychiatry; while their use in Pediatrics is limited by a reliance on radioactive labeled tracers (radioligand). Functional MRI, on the other hand has several unique advantages in that it is a non-invasive technique with improved spatial resolution that permits a more accurate elucidation of the dynamic brain changes associated with each of these neural based developmental disorders. Since there also exists a spectrum of phenotypic heterogeneity among these disorders, it is important to develop such a diagnostic tool that can first identify underlying biological substrates, and then distinguish successful pharmacological or behavioral interventions. The hope of early diagnosis for these neurodevelopmental disorders may ultimately rely on an integration of comprehensive fMRI brain atlases with specific genetic testing. Discussion. This review focuses in the contributions made by studies employing functional MRI to the understanding of Mental Retardation (Joubert Syndrome, Williams Syndrome,Velocradiofacial Syndrome and Fragile X), Pervasive Developmental Disorder, Autism, and Dyslexia.