Botulinum toxin type A (BoNT/A), a neurotoxin that causes flaccid muscle paralysis, is used to control involuntary movements and spasms in dystonia and spasticity. However, beneficial motor effects in these disorders and their duration cannot be explained by the exclusive paralytic action of the toxin on neuromuscular junctions, while recent studies suggest possible central effects. Therefore, here we investigated the central effect of toxins on behavioral indicators of motor function. Rats were bilaterally injected with BoNT-A in m. gastrocnemius (2 U/kg) or n. ischiadicus (5 U/kg). To investigate the role of BoNT-A transcytosis in central synapses, animals were injected intrathecally with antitoxin (5 i.u.). The effect of BoNT-A was examined by various motor tests to evaluate flaccid paralysis, gait and swimming, endurance, coordination and muscle atrophy, but also by immunohistochemical detection of its enzyme product in the spinal cord sections. The combination of the peripheral and central effects of BoNT-A was found to be more intensive and longer than its isolated peripheral effect. The central effects of transcytosis-mediated BoNT-A are mainly limited to cholinergic synapses of spinal interneurons. These findings suggest that the central action intensifies and prolongs the duration of the effect of BoNTA on rat motor functions. Therefore, the longevity of the clinical effects of the toxin and its main therapeutic goal to control muscle activity and tone could depend on its central action.