Research in pediatric central nervous system pathophysiology is focused around three primary goals: identification of neurodevelopmental disorders, understanding the differences in brain development which underlie these disorders, and improving treatment for these young children. Autism spectrum disorders (ASDs) are a complex set of disorders which are characterized by difficulties in language and social interactions. These behavioral measures are highly variable and a number of underlying causes can generate similar behavioral effects. Therefore, it is important to identify neurophysiological markers to better identify and characterize these disorders. Recent ASD findings using MEG show atypical latency and amplitude responses and poor cortical connectivity in children with ASDs across the cognitive spectrum from basic auditory processing, multisensory integration, to face and semantic processing. These results further support the view that ASDs are a complex neurologically-based disorder. On the other hand, the cause of Down syndrome is well understood as originating from a partial or full replication of chromosome 21. However, the cognitive and neurological consequences of this chromosomal abnormality are not yet well understood. Using a simple observation and motor execution task, poor functional connectivity in sensory-motor areas, particularly in the gamma band range, has been identified in children with Down syndrome and is consistent with behavioral deficits in the sensory-motor realm. Additional studies are needed to better understand whether targeted identification of these abnormalities can facilitate treatment in this disorder. Finally, while epilepsy can be reliably diagnosed, seizure control is still limited in many cases where the seizure onset zone is not readily apparent. Advances in pre-surgical evaluation and intra-operative co-registration will be described. These studies describing pediatric CNS pathophysiology will be discussed.