Identifying atypical trajectories that distinguish children with differing developmental disorders from each other and from typically developing children is a potentially powerful tool for early ascertainment and treatment of syndrome specific proficiencies and deficiencies. The past decade has seen unparalleled advances in the fields of molecular genetics, pediatrics, developmental cognitive neuroscience and brain imaging. Collaboratively, these advances have facilitated our understanding of how genes can impact upon early development, through the identification of specific patterns of cognitive and behavior processing and the deficits in these domains that are typical to a specific developmental disorder. These advances have also made early diagnoses possible for many developmental disorders, including those for which genetic etiology has yet to be determined, such as is the case for most individuals with autism, or disorders such as fragile X syndrome that result from the silencing of a single gene. This early identification necessitates thorough investigation of the impact of a condition across the lifespan beginning in early childhood when interventions are most likely to have significant benefit. This is especially relevant for disorders that at first glance appear to share overlapping behavioral and clinical symptomology. In the case of autism and fragile X syndrome, commonalties in social and communication profiles are now well documented in early childhood. However, to what degree symptom overlap implies common developmental pathways or etiologies remains unclear. The focus of this review will be to critically evaluate whether so called commonalities in phenotypic outcomes actually reflect very different developmental pathways that diverge over developmental time and across syndromes. More detailed knowledge of these profiles will facilitate early timing of tailored interventions that will promote optimal development resulting in significant educational, clinical, and adaptive benefits across a childs lifespan.