Purpose: We compared heart rate variability parameters between patients with spina bifida and a control group during urodynamic studies, with the goal of evaluating the autonomic nervous system dysfunction present in spina bifida. Methods: Continuous heart rate variability parameters were recorded during 3 successive periods (P0, the 2 minutes prior to the start of filling; P1, from the start of filling to the first desire to void; and P2, from P1 to the end of filling or the start of voiding). The control group consisted of children with vesicoureteral reflux who had undergone video-urodynamic studies. Our study included 11 patients with spina bifida and 9 control participants. Results: At baseline, patients with spina bifida exhibited lower values for the root mean square of successive differences in NN intervals, the percentage of successive R-R interval differences exceeding 50 msec relative to the total number of intervals, and high frequency (HF). In contrast, the low frequency (LF)/HF ratio was elevated in these patients (5.04 ± 4.75 vs. 0.67 ± 0.42, P = 0.014). During bladder filling, LF/HF values increased in the control group (P0, 0.67 ± 0.42; P1, 0.89 ± 0.34; P2, 1.21 ± 0.64; P = 0.018), while they declined in patients with spina bifida (P0, 5.04 ± 4.75; P1, 3.96 ± 4.35; P2, 3.26 ± 4.03; P < 0.001). The HF values were significantly elevated in children with spina bifida during bladder filling (P = 0.002). In the time domain, the standard deviations of all NN intervals were elevated only in the control group during bladder filling. Parasympathetic activity domains were reduced in the children with spina bifida at the initial assessment. Conclusions During the bladder filling phase, parasympathetic activity increased along with fixed sympathetic activity in the spina bifida group. In contrast, the control group exhibited a shift towards a sympathetic preponderance at the conclusion of bladder filling. These observations may be associated with the pathophysiology of neurogenic bladder in spina bifida.