BACKGROUND: Systemic thromboembolism is a serious, major complication in patients with an atrial septal aneurysm (ASA). Atrial dysfunction resulting from paroxysmal atrial fibrillation is more common in patients with ASA than in the general population. The autonomic nervous system plays an important role in the initiation of atrial fibrillation. OBJECTIVE: To investigate autonomic function and its impact on ventricular and atrial arrhythmia in a group of ASA patients compared with a control group of healthy volunteers. METHODS: The study group consisted of 40 patients with ASA; the control group consisted of 30 age-, sex- and body mass index-matched healthy volunteers. All patients and control subjects underwent echocardiographic examination. Autonomic function was assessed by determining heart rate variability (HRV) indexes. RESULTS: HRV time and frequency domain indexes were lower in patients with ASA compared with healthy controls (188+/-32 ms(2) and 323+/-42 ms(2) for low-frequency HRV; 195+/-39 ms(2) and 377+/-43 ms(2) for high-frequency HRV; P<0.001 for all). Statistically significant differences with respect to other HRV indexes were also found between the two groups. CONCLUSION: ASA appears to be associated with cardiac autonomic dysfunction; however, the mechanisms of this association are not known in detail.