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Autism spectrum disorder is a complex, heterogeneous neurodevelopmental condition of largely unknown etiology. This heterogeneity of symptom presentation, combined with high rates of comorbidity with other developmental disorders and a lack of reliable biomarkers, makes diagnosing and evaluating life outcomes for individuals with autism spectrum disorder a challenge. We review the growing literature on neuroimaging-based biomarkers of risk for the development of autism and explore evidence for resilience in some autistic individuals. The current literature suggests that neuroimaging during early infancy, in combination with prebirth and early genetic studies, is a promising tool for identifying biomarkers of risk, while studies of gene expression and DNA methylation have provided some key insights into mechanisms of resilience. With genetics and the environment contributing to both risk for the development of autism spectrum disorder and conditions for resilience, additional studies are needed to understand how risk and resilience interact mechanistically, whereby factors of risk may engender conditions for adaptation. Future studies should prioritize longitudinal designs in global cohorts, with the involvement of the autism community as partners in research to help identify domains of functioning that hold value and importance to the community.