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To assess heart rate variability (HRV) in athletes with concussion across three phases of recovery.A prospective matched control group design included the collection of HRV and symptoms measured by the Rivermead Post-Concussion Questionnaire. These measures were taken at 3 phases of recovery [(1) symptomatic; (2). asymptomatic; and (3) one-week after return-to-play (RTP)]. The same protocol was completed by noninjured athletes.Interuniversity sports teams at a single institution.11 athletes, across 7 sports, diagnosed with concussion, and 11 matched-athlete controls volunteered for the study.Physician diagnosed concussion and a sitting to standing protocol for HRV monitoring.The frequency, time, and nonlinear domains of HRV were assessed along with the absolute difference between sitting and standing for each.A 2 x 3 (group x phase) repeated-measures analysis of variance revealed significant interactions for sitting High Frequency (HF) norm, sitting Low Frequency (LF) norm, the difference between sitting and standing HF norm, and difference between sitting and standing LF norm. Acutely, athletes with concussion displayed increased LF norm and decreased HF norm while sitting and a decreased change in their HF and LF norm measures between sitting and standing. A significant group effect for sample entropy when standing was detected, with the concussed group displaying decreased values compared with the matched controls.Athletes with concussion displayed autonomic dysfunction in some measures of HRV that persisted beyond RTP and were related to a previous history of concussion.