There is a paucity of data regarding the significance of left atrial (LA) volume and its changes throughout the cardiac cycle in pediatric patients with heart disease. The recently developed LA volume-tracking (LAVT) method can automatically construct the LA volume curve. The study group consisted of 48 pediatric patients with ventricular septal defect (n = 34) or patent ductus arteriosus (n = 14) and age-matched healthy controls. Maximum and minimum LA volumes (LAVmax and LAVmin, respectively) were measured. The total LA emptying volume (LAVtotal) was defined as LAVmax − LAVmin. Volume parameters were standardized by dividing by body surface area (BSA). The total LA emptying fraction (%LAVtotal) was defined as the ratio of LAVtotal to LAVmax. In the patient group, there was a positive correlation between the ratio of pulmonary to systemic blood flow (Qp/Qs) and LAVmax/BSA, LAVmin/BSA, and LAVtotal/BSA (r = 0.42, 0.44, and 0.34, respectively). LAVmin/BSA was positively correlated with the ratio of early mitral inflow velocity to early mitral annular diastolic tissue Doppler velocity (E/E′) (r = 0.32). The %LAVtotal had a negative correlation with left-ventricular (LV) end-diastolic pressure (r = −0.32). There were significant correlations between serum B-type natriuretic peptide level and LAVmax/BSA, LAVmin/BSA, and %LAVtotal (r = 0.38, 0.49, and −0.35, respectively). The LAVT method is useful in the evaluation of LV diastolic function in pediatric patients with chronic LV volume overload.