PRIMARY OBJECTIVE: To investigate disconnection theories postulated as the cause of dysautonomia following severe traumatic brain injury (TBI) through analysis of heart rate variability (HRV). METHODS AND PROCEDURES: Data were collected on age-matched subjects with and without dysautonomia (eight subjects in each group) and 16 non-injured controls. Data included injury details, continuous electrocardiograph recordings and rehabilitation outcome. MAIN OUTCOMES AND RESULTS: The TBI group revealed significant differences in HRV parameters both compared to controls and between dysautonomic and non-dysautonomic subjects. Additionally, HRV parameters for dysautonomic subjects showed evidence of an uncoupling of the normal relationship between heart rate and sympathetic/parasympathetic balance. HRV changes persisted for the dysautonomia group for a mean of 14 months post-injury. CONCLUSIONS: Dysautonomic subjects revealed prolonged uncoupling of heart rate and HRV parameters compared to non-dysautonomic subjects and controls. These findings represent direct pathophysiological evidence supporting the disconnection theory postulated to produce dysautonomia following TBI.