BACKGROUND: Heart rate variability (HRV) is a sign of the cardiac autonomic nervous system. Its evaluation in pediatric ventricular septal defect (VSD) cases before and after transcatheter closure contributes to an understanding of cardiac autonomic control. METHODS: Nineteen children with VSDs treated with transcatheter closure and 18 healthy children were enrolled in this study. A 24-h Holter rhythm monitor was applied to all patients before VSD closure and to those in the control group. Holter rhythm monitoring was repeated at three months in the patient group. HRV parameters were measured using the Cardio Scan Premier 12(R) program. Frequency-domain (total power; very-low-frequency, low-frequency (LF), and high-frequency (HF) indices; and the LF/HF ratio) and time-domain (standard deviation of all RR intervals (SDNN), standard deviation of 5-min averages of RR intervals (SDANN), the SDNN index, percentage of the difference between adjacent RR intervals, and the square root of the mean of the sum of square differences between adjacent filtered RR intervals) parameters were assessed. RESULTS: Before the procedure, SDNN, SDANN, and total power values were lower in the patient group than in the control group; other parameters were similar in the two groups. No significant difference in the SDNN, SDANN, or total power was detected between the patient and control groups in the third month, indicating that autonomic control of patients\' hearts became normal during the third postoperative month. No correlation was detected between any hemodynamic parameters and any time-domain or frequency-domain parameters before closure. CONCLUSION: This study showed that transcatheter closure of VSDs changed HRV parameters in pediatric patients.