Background: We hypothesized that patients with atrial (ASD) and ventricular septal defects (VSD) have similarly reduced heart rate variability (HRV) since both defects cause similar increases in pulmonary blood flow and right ventricular filling pressure. We examined the correlation between HRV and respiratory frequency (RSA) characteristics and left‐to‐right shunt ratio (Qp/Qs) measured by Doppler echocardiography. Methods: The study included 83 patients with diagnoses of ASD (n = 43) or VSD (n = 40). The electrocardiogram and respiratory waves were recorded during Doppler echocardiography test, and HRV was measured to calculate the low frequency (LF), high frequency (HF), total frequency (TF), and RSA components, and the LF/HF, RSA/TF, and LF/RSA ratios. Qp/Qs was calculated from Doppler echocardiography and its relationship with HRV parameters was examined by multivariate analysis. Results: There was a positive correlation between Qp/Qs and LF/RSA in the ASD group, and a negative correlation in the VSD group. In contrast, Qp/Qs correlated negatively with RSA/TF in the ASD group, and positively in the VSD group. Conclusion: Different effects of respiratory vagal activity on HRV were observed in patients with ASD versus VSD.