ObjectiveTo compare prospective ECG-gated multi-slice computed tomography (MSCT) and trans-thoracic echocardiography (TTE) in the diagnosis of complex congenital heart disease (CHD).MethodsThis was a prospective study of consecutive patients with complex CHD (age <7 years) treated at a tertiary hospital between May 2013 and May 2015. All patients were imaged with TTE and prospective ECG-gated 128-slice spiral CT in the week before surgery. Effective radiation dose (ED) was calculated from volume CT dose index (CTDIvol) and dose length product (DLP). Image quality (5-point scale) was assessed independently by two radiologists. Using surgical findings as the reference, the diagnostic capabilities of MSCT and TTE were compared.ResultsThirty-five patients (19 males) aged 1.59±1.58 years (range, 3 days to 74 months) were included. CTDIvol, DLP and ED were 0.90±0.24 mGy, 12.9±4.7 mGy∙cm and 0.64±0.21 mSv (range, 0.358–1.196 mSv), respectively. Image quality score was 4.3±0.5, and all images met the diagnostic requirements. The sensitivity, specificity, positive predictive value, and negative predictive value for diagnosing CHD were 97.2%, 99.8%, 99.0%, and 99.5%, respectively, for MSCT, and 90.6%, 99.8%, 99.0%, and 98.4%, respectively, for TTE. MSCT not only had a higher sensitivity than TTE overall (97.2% vs. 90.6%; P<0.05), but was much more sensitive for the diagnosis of extracardiac vascular abnormalities (92.0% vs. 68.0%; P<0.05).Conclusion128-slice low-dose prospective ECG-gated CT scanning has important clinical value in the diagnosis of complex CHD in children, complementing and extending the findings of TTE.