Acute ischemic stroke, especially minor stroke, and transient ischemic attack have high risks of recurrence and exacerbation into severe ischemic strokes. It remains challenging to perform risk stratification and screen high-risk groups for initiation of early treatment in these patients. Moreover, with the growing population of patients with chronic small vessel disease, the mechanisms and clinical implications require further investigation. Traditional tools such as the ABCD2 score (age, blood pressure, clinical features, duration of symptoms, diabetes) have only moderate predictive value in patients with transient ischemic attack or minor stroke. By contrast, measurement of changes in heart rate variability (HRV) is an important and novel tool for risk stratification and outcome prediction in patients with cardiovascular diseases, as it reflects the overall level of autonomic nervous system dysfunction. Thus, abnormal HRV may be useful for prognosis and improve stratification of stroke patients with diverse risks. HRV may also partially explain autonomic nervous dysfunction and other manifestations during the process of chronic cerebral small vessel disease. In summary, measurement of HRV may contribute to early initiation of interventions in acute or chronic stroke patients using novel treatments involving rebalancing of autonomic nervous system function.