OBJECTIVES: To assess cardiovascular autonomic nervous system function of patients post-brain-injury in the sub-acute phase during a physiotherapy session (PTS). PARTICIPANTS: Fourteen patients post-ischaemic stroke and 11 post-severe traumatic brain injuries. INTERVENTION: Continuous electrocardiogram recording at rest, during active cycling and during routine PTS. MAIN OUTCOME MEASURE: Heart rate (HR) and Heart rate variability (HRV) parameters included the standard deviation of all R-R intervals (SDNN), the square root of the mean squared differences of successive differences (RMSSD), the Low-frequency (LF) power, High-frequency (HF) power and the LF/HF ratio. RESULTS: The median HR at rest was 76 bpm (interquartile range 61-81). Significant increments were noted during activities; median HR during cycling was 93 bpm, during the most intense activity 91 bpm (p-value < 0.001). A significant decline in HRV parameters\' median values during cycling and PTS was observed only among patients post-stroke. CONCLUSIONS: Among patients post-brain injury, HR increased significantly during PTS in different activities and varied positions; therefore, therapists should be aware and monitor HR frequently during training. In addition, HRV values were low at rest and did not respond to activity among patients post-TBI, compared with higher values at rest and some response among patients post-stroke. This may indicate that autonomic impairment post-brain insult is more likely a consequence of central nervous system damage and less likely a result of pre-event cardiovascular illness.