Botulinum toxin (BTX) is the treatment of choice for blepharospasm. To investigate if the locally injected BTX influences the central nervous system and in particular the brain stem, amplitude and latency of compound muscle action potential (CMAP) of orbicularis oculi, blink reflex and brain stem auditory evoked potential were studied in 12 blepharospasm patients before BTX therapy, 9 patients after BTX therapy and 9 age and sex matched healthy controls. The mean amplitude of orbicularis oculi in patients was significantly lower before BTX therapy (p < 0.05) and after BTX therapy (p < 0.02). The amplitudes of R1, R2 and contralateral R2 (CR) was higher in patients than controls but did not reach statistical significance. Following BTX therapy there was a reduction in amplitude of R1, R2 and CR (p < 0.001) and prolongation of latency of R2 and CR (p < 0.05). The ratio of blink reflex amplitude/CMAP amplitude of orbicularis oculi showed a significant decline after BTX therapy (p < 0.01). This small study suggests the involvement of brain stem pathways following BTX therapy in patients with blepharospasm.