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Number of imaging studies of neurodevelopmental disorders (NDDs) has grown recently.Methodological and conceptual challenges remain in neuroimaging research of NDDs.Poor replicability and generalizability hinder translational goals of NDD research.This study discusses challenges and advances in neuroimaging research of three NDDs.Neuroimaging can find markers that can assist with NDD diagnosis and treatment.Recent years have witnessed the proliferation of neuroimaging studies of neurodevelopmental disorders (NDDs), particularly of children with autism spectrum disorder (ASD), attention-deficit/hyperactivity disorder (ADHD), and Tourette's syndrome (TS). Neuroimaging offers immense potential in understanding the biology of these disorders, and how it relates to clinical symptoms. Neuroimaging techniques, in the long run, may help identify neurobiological markers to assist clinical diagnosis and treatment. However, methodological challenges have affected the progress of clinical neuroimaging. This paper reviews the methodological challenges involved in imaging children with NDDs. Specific topics include correcting for head motion, normalization using pediatric brain templates, accounting for psychotropic medication use, delineating complex developmental trajectories, and overcoming smaller sample sizes. The potential of neuroimaging-based biomarkers and the utility of implementing neuroimaging in a clinical setting are also discussed. Data-sharing approaches, technological advances, and an increase in the number of longitudinal, prospective studies are recommended as future directions. Significant advances have been made already, and future decades will continue to see innovative progress in neuroimaging research endeavors of NDDs.