In this study, we investigated the relationship between plasma B-type natriuretic peptide (BNP) levels and hemodynamics from cardiac catheterization in pediatric patients with atrial or ventricular septal defect. A total of 59 patients were studied including 80% of patients had Qp/Qs > 1.5 and 25% of patients had pulmonary hypertension. The mean BNP value and BNP z-score were 10.9 ± 11.2 pg/mL and -0.28 ± 1.7 (-2.85 to 3.29), respectively. There was a statistically significant linear correlation between BNP value and the size of defects (r = 0.303, p = 0.002) and a trend toward to positive correlation between BNP value and Qp/Qs ratio (r = 0.183, p = 0.166) among all patients. To identify patients with a Qp/Qs ratio >1.5, the sensitivity and specificity were 28%, 100% in all patients at a plasma BNP cut-off point of 15 pg/mL. We concluded that a BNP > 15 pg/mL would help identify patients who need further intervention.