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Sport-related concussions are associated with a range of physical, cognitive, and behavioral disturbances that are highly variable across individuals. Much remains unknown about the effects of sport concussion, and changes in markers of psychological and physiological stress over the recovery timeline.To examine psychological (mood, stress, sleep quality, and symptoms) and physiological (heart rate variability and salivary cortisol) measures in concussed athletes over clinical recovery milestones.University athletic program, sport medicine clinic, Canada.A sample of 52 interuniversity athletes (32 male and 20 female), 26 with concussion and 26 healthy controls.Case-control repeated measures study at 3 time points of the clinical recovery process. Measures were administered to a matched control sample of uninjured athletes as well.Physiological measures were heart rate variability and salivary cortisol; psychological measures were mood, perceived stress, and quality of sleep.Psychological measures were significantly worse for concussed athletes relative to controls at the symptomatic phase (acute injury), but significantly better at return-to-play (RTP). Multivariate analysis of heart rate variability identified main effects of sex and concussion, with reduced high-frequency heart rate variability for females and concussed athletes extending into the post-RTP phase. An interaction effect was also observed, showing the cardiac response of female athletes was more sensitive to concussion compared with males. Conversely, male athletes showed greater suppression of low-frequency heart rate variability associated with mood disturbances.This integrated study of psychological and physiological markers in concussed athletes confirmed the resolution of mood disturbances, symptoms, and sleep quality by RTP, but identified autonomic nervous system disturbances, as measured by depressed heart rate variability beyond RTP.