The vulnerability-stress model is a hypothesis for symptom development in schizophrenia patients who are generally characterized by cardiac autonomic dysfunction. Therefore, measures of heart rate variability (HRV) have been widely used in schizophrenics for assessing altered cardiac autonomic regulations. The goal of this study was to analyze HRV of schizophrenia patients and healthy control subjects with exposure to auditory stimuli. More specifically, this study examines whether schizophrenia patients may exhibit distinctive time and frequency domain parameters of HRV from control subjects during at rest and auditory stimulation periods. Photoplethysmographic signals were used in the analysis of HRV. Nineteen schizophrenic patients and twenty healthy control subjects were examined during rest periods, while exposed to periods of white noise (WN) and relaxing music. Results indicate that HRV in patients was lower than that of control subjects indicating autonomic dysfunction throughout the entire experiment. In comparison with control subjects, patients with schizophrenia exhibited lower high-frequency power and a higher low-frequency to high-frequency ratio. Moreover, while WN stimulus decreased parasympathetic activity in healthy subjects, no significant changes in heart rate and frequency-domain HRV parameters were observed between the auditory stimulation and rest periods in schizophrenia patients. We can conclude that HRV can be used as a sensitive index of emotion-related sympathetic activity in schizophrenia patients.