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The auditory startle response (ASR) is a brainstem reflex elicited by an unexpected acoustic stimulus. In focal dystonia (FD), the excitability of brainstem neurons is abnormally enhanced. To identify a possible impact of this pathology on the processing of acoustic stimuli, we studied the habituation of the ASR in patients (n = 11) with FD and compared the findings to those of patients with Parkinson's disease (PD; n = 11) and controls (n = 11). Latencies in FD patients did not differ from those of controls but were delayed in PD patients compared to controls (p < 0.0001). Habituation was normal at the orbicularis oculi muscles but reduced at the sternocleidomastoid muscles in FD (p = 0.005). Habituation in PD was comparable to controls. Normal latencies and sequence activation indicate intact neural pathways mediating the ASR in FD. Impaired habituation of the ASR points towards a reduced inhibition of acoustic stimuli in FD.