Three-dimensional echocardiography (3DE), a novel approach employed in detecting congenital heart disease (CHD), has gained popularity since it was made commercially available in 2002. This modality is now accepted as an important diagnostic tool for diagnosing CHD. Advancement in transducer technologies and digital data processing allows the use of 3DE in daily clinical practice. In this review, modes of 3DE data acquisition and storage methods in the echocardiogram’s machine’s hard disk (data processing) are examined. Analysis of the acquired data (cropping or slicing the data set) and methods of illustrating the cropped data set for cardiologists and pediatric cardiovascular surgeons are also discussed. Published literature was searched in PubMed using the keywords “three-dimensional echocardiography”, “congenital heart disease”, “cropping”, and “echoangiogram”. This search produced 100 articles, which were further short-listed to 30 articles. Based on this algorithm, the final selected 30 articles were extensively examined in the current review. The clinical applications of real-time transthoracic 3DE, as well as novel transesophageal 3DE and color flow 3DE data set analyses (echoangiogram) in the routine practice of CHD assessment, are also reviewed. Finally, the limitations 3DE, together with the potential future developments required to improve various techniques of 3DE to make it more readily applicable, are examined.