Echocardiography, CT and MRI have a crucial role in the management of congenital heart disease (CHD) patients. All of these modalities can be presented in a 2D or a 3D rendered format. The aim of this paper is to review the key advantages and potential limitations, as well as the future challenges of a 3D approach in each imaging modality. The focus of this review is on anatomic rather than functional assessment. Conventional 2D echocardiography presents limitations when imaging complex lesions, whereas 3D imaging depicts the anatomy in all dimensions. CT and MRI can visualise extracardiac vasculature and guide complex biventricular repair. Three-dimensional printed models can be used in depicting complex intracardiac relationships and defining the surgical strategy in specific lesions. Extended reality imaging retained dynamic cardiac motion holds great potential for planning surgical and catheter procedures. Overall, the use of 3D imaging has resulted in a better understanding of anatomy, with a direct impact on the surgical and catheter approach, particularly in more complex cases.