Botulinum toxin is a well established, highly effective and safe treatment option for movement disorders and autonomic diseases with excellent long term results. There is increasing evidence that the beneficial effect in both motor and autonomic indication is based on a complex mode of botulinum toxin action modulating efferent as well as afferent nerve fiber activity. In particular, this has been shown for the treatment of dystonia, spasticity and overactive bladder. A unique observation is that botulinum toxin has a markedly longer duration of action in autonomic than in motor disorders for which the reason remains unclear. Although botulinum toxin type B seems to have an initially higher affinity to autonomic nerve endings there is currently no clear evidence that type B is superior to type A in autonomic disorders. The risk of antibody formation probably does not depend on the target tissue injected and seems to be similar for movement disorders and autonomic indications. More research is needed to better understand similarities and differences of treatment outcome in motor and autonomic disorders.