Objectives To determine whether physical activity and participation 1 and 5 years after discharge are associated with measures of cardiovascular autonomic function: prevalence of hypotension and reduced peak heart rate at discharge from initial inpatient spinal cord injury (SCI) rehabilitation. Design Prospective cohort study. Setting Rehabilitation centers. Participants Individuals with SCI (N=146). Interventions Not applicable. Main Outcome Measures We recorded markers of cardiovascular autonomic dysfunction (resting blood pressure and peak heart rate) and personal and lesion characteristics at the time of discharge from rehabilitation. Parameters for participation (social health status dimension of the Sickness Impact Profile) and physical activity (Physical Activity Scale for Individuals with Physical Disabilities [PASIPD]) were measured 1 and 5 years after discharge. Effects of prevalence of cardiovascular autonomic dysfunction were analyzed using linear regression analysis while correcting for possible confounders. Results We found no significant association between hypotension and social health status dimension of the Sickness Impact Profile or PASIPD, either at 1 or at 5 years after discharge. A significant association between peak heart rate and social health status dimension of the Sickness Impact Profile was found at 1 year after discharge, showing poorer participation in individuals with low peak heart rate (ie, cardiovascular autonomic dysfunction). The unadjusted relation between peak heart rate and the social health status dimension of the Sickness Impact Profile was significant at 5 years, but not when adjusted for confounders. We found associations between peak heart rate and PASIPD for both 1 and 5 years after discharge; however, these were not significant after correction for potential confounding factors. Conclusions Autonomic dysfunction after SCI is a crucial factor influencing quality of life. We found that cardiovascular autonomic impairment, assessed from low peak heart rate, was associated with reduced participation after 1 year. The results suggest that peak heart rate at discharge from rehabilitation after SCI should be used to identify those needing additional support to facilitate physical activity and participation after discharge.