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Using methods to improve brainstem imaging in children, this study set out to elucidate the role of the autonomic, nociceptive, and limbic brainstem nuclei in the autism features of 145 children (74 autistic children, 6.0\u201310.9\u2009years). Participants completed an assessment of core autism features and diffusion\u2010 and T1\u2010weighted imaging optimized to improve brainstem images. After data reduction via principal component analysis, correlational analyses examined associations among autism features and the microstructural properties of brainstem clusters. Independent replication was performed in 43 adolescents (24 autistic, 13.0\u201317.9\u2009years). We found specific nuclei, most robustly the parvicellular reticular formation\u2010alpha (PCRtA) and to a lesser degree the lateral parabrachial nucleus (LPB) and ventral tegmental parabrachial pigmented complex (VTA\u2010PBP), to be associated with autism features. 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