Purpose: Reduced heart rate variability significantly increases cardiovascular mortality. Metabolic syndrome increases the cardiac autonomic dysfunction. Recently, increasing cardiovascular mortality has been reported in patients with schizophrenia. This study was done to compare heart rate variability between adults with and without schizophrenia and to compare the relationship of heart rate variability to metabolic syndrome in hospitalized patients with schizophrenia. Methods: This was a descriptive and correlational study in which 719 adults without schizophrenia and 308 adults with schizophrenia took part between May and June 2008. We measured the following: five-minute heart rate variability; high-frequency, low-frequency, the ratio of low-frequency to high-frequency, and the Standard Deviation of all the normal RR intervals. Data was also collected on metabolic syndrome, abdominal obesity, triglycerides, HDL cholesterol, blood pressure and fasting glucose. Results: The Standard Deviation of all the normal RR intervals values of heart rate variability indices were $1.53{pm}0.18$. The low-frequency and high-frequency values of heart rate variability indices were significantly higher in hospitalized patients with schizophrenia ($3.89{pm}1.36$; $3.80{pm}1.20$) than those in the healthy participants ($2.20{pm}0.46$; $2.10{pm}0.46$). There were no significant differences between the schizophrenic patients with and without metabolic syndrome. Conclusion: The results of this study indicate that schizophrenia patients have significantly lower cardiac autonomic control, but they have significantly higher low-frequency and high-frequency values than those of healthy adults. Use of antipsychotic drug may affect the autonomic nervous system in schizophrenic patients. Metabolic syndrome was not associated with cardiac autonomic control in schizophrenia patients.