Several studies have shown various degrees of autonomic dysfunction in patients with multiple sclerosis. Longitudinal follow-up studies are remarkably scarce up to now. We assessed autonomic dysfunction twice with an interval of 1 year in 20 relapsing remitting and 26 secondary progressive MS-patients. Autonomic function was assessed by the heart rate response during deep breathing, standing up and Valsalva manoeuvre. Only the maximum change in heart rate after standing up (in ms and beats/min) and the Max/Min ratio after standing up showed significant worsening over 1 year. The changes in EDSS scores also documented gradual deterioration of the neurological condition over the study period. We conclude that there is progression of autonomic dysfunction in MS over 1 year and that this could correlate with progression in clinical disability.