BACKGROUND: Patients with mitral valve prolapse (MVP) may reveal symptoms of autonomic dysfunction and heart rate variability (HRV). We sought to explore the autonomic nervous system in children with MVP. METHODS: This cross-sectional study enrolled 60 children aged between 5 and 15 years with MVP and 60 age- and sex-matched healthy children as controls. Two cardiologists performed electrocardiography and standard echocardiography. HRV parameters were explored via 24-hour rhythm 3-channel Holter monitoring. The depolarization of ventricular and atrial parameters, comprising QT max and min, QTc intervals, QT dispersion, P maximum and minimum, and P-wave dispersion, was measured and compared. RESULTS: The mean age was 13.12+/-1.50 years in the MVP group (F/M: 34/26) and 13.20+/-1.81 years in the control group (F/M: 35/25). The maximum duration and P-wave dispersion in the MVP group were significantly different from the healthy children (P<0.001). The longest and shortest QT dispersion values and QTc values were significantly different between the 2 groups (P=0.004, P=0.043, P<0.001, and P<0.001, respectively). The HRV parameters were significantly different between the 2 groups, too. CONCLUSION: Decreased HRV and inhomogeneous depolarization showed that our children with MVP were prone to atrial and ventricular arrhythmias. Furthermore, P-wave dispersion and QTc could be used as prognostic markers of cardiac autonomic dysfunction before it is diagnosed by 24-hour Holter monitoring.