OBJECTIVE: It has been documented that impaired heart rate variability (HRV) is related to life threatening arrhythmias in children with surgically repaired congenital heart disease. We aimed to analyze the balance of the cardiac autonomic functions by assessing HRV in children with arterial switch operation (ASO). METHODS: In this observational cohort study, HRV analysis using 24-h Holter electrocardiography recordings was examined in 22 patients (mean age: 59.5+/-38.7 months, 18 male, 4 female) who had undergone ASO during the newborn period and 22 healthy children (mean age: 65.1+/-39.4 months, 18 male, 4 female). After Kolmogorov-Smirnov testing for normality, Student t-test and Mann-Whitney U test were used when appropriate. Chi-square was used for categorical data. RESULTS: In 24-h HRV analysis showed that SDANN and VLF were significantly higher in patient group. Awake SDNN, rMSSD, pNN50, TP and VLF levels of patient group were significantly higher than those of control subjects. Awake LF/HF ratio in patient group was significantly higher than their counterpart in asleep group. In the patient group, awake rMSSD, pNN50, TP, LF and HF were significantly lower than their counterpart in the asleep group. CONCLUSION: Children with transposition of the great arteries (TGA) following ASO have not decreased levels of time and frequency HRV parameters in the mid-term follow-up period. All HRV parameters reflecting vagal tone were increased in the patient group. It is suggested that vagal tone is more predominant than sympathetic tone for children with ASO.