Anomalies of the coronary arteries are commonly associated with congenital heart disease (CHD). Anomalies include variations in number, shape, and location of the origin, as well as the course of the coronary artery. An intramural course of one of the coronary arteries is a rather rare condition. Most cases of anomalies are of no clinical relevance and are found incidentally during evaluation for other cardiac conditions. However, they become of importance when cardiac surgery/intervention, especially valve replacement, needs to be performed. We conducted a literature review for coronary anomalies with an intramural course in patients with CHD and include three cases from our own clinic. Note that transposition of the great arteries seems to be the condition most frequently associated with an intramural course of one of the coronary arteries. In case of a suspected anomaly, transesophageal echocardiography presents a valuable tool to visualize the origin and course of the coronary artery, as well as the relationship to important anatomical structures like the aortic or pulmonary valve. Alternatively, cardiac magnetic resonance imaging can be used. Although rare, both cardiologists and surgeons need to be aware of intramural courses of coronary arteries to prevent accidental trauma to them and thereby, reducing the risk for the patient.