Neurocardiac dysregulation has been reported in schizophrenia. Indices of heart rate variability (HRV) are useful in assessing the status of cardiac autonomic regulation. We explored within-subject changes in HRV indices in acutely ill patients with schizophrenia treated with risperidone. Sixteen medication-naive or medication-free patients with DSM-IV schizophrenia completed electrocardiogram (ECG) assessments at baseline and after six weeks of treatment with risperidone. Indices of HRV were extracted from 5-min resting ECG recordings and compared to those obtained from control subjects matched for age and gender. Psychiatric and drug-induced extrapyramidal symptoms were assessed by the Positive and Negative Syndrome Scale (PANSS) and the Drug-Induced Extrapyramidal Symptoms Scale (DIEPSS). In comparison with matched controls, patients with acute schizophrenia showed lower values of time-domain measures, lower high-frequency power (HF) and a higher ratio of low to high frequency (LF/HF). In the within-subject analyses, a significant decrease in LF/HF was associated with risperidone treatment. In addition, LF/HF, which initially co-clustered with clinical variables, congregated with other HRV measures after the six-week risperidone treatment. These results indicate that, in the therapeutic process, risperidone treatment may exert a beneficial influence on the sympathovagal imbalance in acute schizophrenia.