BACKGROUND: Autonomic nervous system (ANS) imbalance has been reported in a number of psychiatric disorders such as depression, schizophrenia, panic disorder, etc. Autonomic dysfunction in schizophrenia has been associated with the symptoms and manifestation of psychosis. Heart rate variability (HRV) as a tool has been widely used to assess ANS activity and the effect of disease on the sympathovagal balance. Therefore, in the present study, HRV derived from electrocardiogram (ECG) lead II at rest was investigated in order to understand the changes in frequency domain measures in patients with schizophrenia and their first-degree relatives compared to healthy controls. METHODS: Twenty-five patients with schizophrenia, 24 first-degree relatives of patients, and 24 healthy controls (Diagnostic and Statistical Manual of Mental Disorders (DSM)-5; 18-45 years) were included in the study. HRV of the subjects was measured after five minutes of rest. ECG lead II was recorded for five minutes and HRV was analysed in the frequency domain: low frequency (LF), high frequency (HF), total power, and LF/HF ratio. HRV parameters and heart rate were statistically analysed for group comparisons using general linear model multivariate analysis. RESULTS: Patients had significantly higher minimum heart rate and lower HF (normalized units (nu)) compared to their first-degree relatives. A trend was observed in HF (nu) with the lowest in patients followed by healthy controls and first-degree relatives and LF/HF ratio was the highest in patients followed by healthy controls and first-degree relatives, although not statistically significant. No significant difference was found between first-degree relatives and healthy controls. CONCLUSION: The alteration of HRV in schizophrenia could be attributed to reduction in vagal tone and sympathetic dominance, which in turn could serve as state markers of schizophrenia.