Advances in biomedical engineering have led to three-dimensional (3D)-printed models being used for a broad range of different applications. Teaching medical personnel, communicating with patients and relatives, planning complex heart surgery, or designing new techniques for repair of CHD via cardiac catheterisation are now options available using patient-specific 3D-printed models. The management of CHD can be challenging owing to the wide spectrum of morphological conditions and the differences between patients. Direct visualisation and manipulation of the patients’ individual anatomy has opened new horizons in personalised treatment, providing the possibility of performing the whole procedure in vitro beforehand, thus anticipating complications and possible outcomes. In this review, we discuss the workflow to implement 3D printing in clinical practice, the imaging modalities used for anatomical segmentation, the applications of this emerging technique in patients with structural heart disease, and its limitations and future directions.