Background: The study aimed to assess sensitivity, specificity and accuracy of CT scan in diagnosing various cardiovascular anomalies in patients with complex congenital heart disease; to obtain additional information in pre-operative patients, inconclusive on echocardiography; and to compare results of multi-detector computed tomography (MDCT) with cardiac catheter angiography (CCA) in accurately delineating the cardiovascular morphological features and to determine if MDCT can replace diagnostic CCA in evaluation of complex CHD.Methods: In this prospective, comparative, single-centre study, a total 50 patients were included in the study aged between 6 days to 17 years. All patients were referred by pediatric cardiologists between August, 2014 and November, 2016. All patients had undergone initial echocardiography and final diagnosis was confirmed by comparing MDCT data with CCA.Results: Total of 177 cardiovascular anomalies are found in our study of 50 patients out of these 3 cases of VSD and one case of ASD was missed on CT angiography and its overall accuracy as compared to catheter angiography was found to be 97.1% Its accuracy in evaluation of TOF, DORV, TAPVC, TA TGA, COA, right sided aortic arch, MAPVC, persistent SVC, PDA, PS, vascular sling and coronary cameral fistula was 100%.Conclusions: The MDCT is found comparable to CCA in the diagnosis of extra cardiac vascular anomalies but the overall sensitivity in the diagnosis of intra-cardiac anomalies is little lower. It can be used as a substitute to CCA in complex CHD and is very helpful tool in preoperative planning and postoperative follow-up.