ObjectiveTo compare radiation dose, contrast enhancement, image noise and heart rate variability in electrocardiography (ECG)-gated computed tomography (CT) ventricular volumetry using a three-dimensional (3D) threshold-based segmentation between the conventional single scan and dual focused scan methods in patients with congenital heart disease. MethodsAfter matching for age, sex, heart rate during the CT examination, and tube voltage, 96 patients (age range, 7 − 36 years; male:female = 63:33) who underwent ECG-gated CT volumetry using a 3D threshold-based segmentation, were divided into 32 patients who underwent a conventional single scan (group 1) and 64 who underwent dual focused scans (group 2). CT radiation dose, contrast enhancement, image noise, and heart rate variability were compared between the two groups. ResultsVolume CT dose index, dose-length product, and effective dose estimates, in group 1 were significantly higher than those in group 2 (28.4 ± 24.6 mGy vs. 9.7 ± 4.5 mGy, 636.5 ± 572.9 mGy cm vs. 379.5 ± 192.4 mGy cm, 8.9 ± 8.0 mSv vs. 5.3 ± 2.7 mSv, 8.2 ± 6.4 mSv vs. 5.0 ± 2.2 mSv, respectively; p values < 0.019). No significant differences in right and left ventricular contrast enhancement were found between the two groups (470.2 ± 152.4 HU vs. 481.0 ± 139.2 HU and 428.6 ± 97.8 HU vs. 429.3 ± 106.7 HU, respectively; p values > 0.05). Image noise measured in the air showed no significant differences between groups 1 and 2 (5.6 ± 1.9 HU vs. 5.5 ± 1.1 HU; p > 0.05). The proportion of heart rate variability ≥ 20 beats per minute in group 1 (15.6 %, 5/32) was significantly higher than that in group 2 (3.1 %, 2/64; p < 0.040). ConclusionCompared with the conventional single scan method, the dual focused scan method can provide a lower radiation dose with comparable contrast enhancement and image noise for ECG-gated CT ventricular volumetry using a 3D threshold-based segmentation in patients with congenital heart disease.