Patients with schizophrenia exhibit impairments in prepulse inhibition (PPI) of the startle response. Available data suggest that atypical antipsychotics may be more effective than typical antipsychotics in improving PPI deficits in schizophrenia. However, previous studies have used between-subjects rather than longitudinal within-subjects designs to demonstrate superiority of particular atypical antipsychotics over typical antipsychotics in improving PPI in patients with schizophrenia. This longitudinal within-subjects test-retest study was designed to evaluate changes in PPI and clinical symptoms in patients with schizophrenia after switching from the conventional antipsychotic zuclopenthixol to long-acting injectable risperidone. PPI was measured in 45 chronic male patients with schizophrenia treated with zuclophentixol depot (session T1), and 12 weeks after switching to long-acting injectable risperidone (session T2). Thirty-six healthy control subjects were also evaluated. Patients with schizophrenia showed a significant improvement in PPI after changing to long-acting risperidone. Improvement of PPI deficits between T1 and T2 assessments correlated significantly with improvements in PANSS general psychopathology subscale scores. Our findings indicate that long-acting risperidone improves PPI deficits in subjects with chronic schizophrenia. These results also suggest that the PPI-restoring effect of risperidone may be related to improvement in symptoms other than positive and negative symptoms.