The heart is the organ responsible for pumping blood throughout the body. The normal heart has a right side and left side, separated by a wall (septum). Each side is further divided into an upper collecting chamber (atrium) and lower pumping chamber (ventricle). A series of valves located in the heart help regulate blood flow in the right direction. Arteries are the large blood vessels, which take blood away from the heart; veins are blood vessels returning blood to the heart.

Normally, the right atrium receives blood returning from the body. This blood is low in oxygen, giving it a bluish color. It flows to the right ventricle, and is then pumped out of the pulmonary artery to the lungs. In the lungs it picks up fresh oxygen and becomes bright red. This "red blood" then flows through the pulmonary veins to the left atrium and into the left ventricle. It is then pumped out of the aorta to the rest of the body, delivering oxygen and nutrients. Once oxygen is delivered to and extracted by the body tissues, the "blue blood" returns through the veins to the right atrium, beginning the cycle again.

In congenital heart disease any of these veins, valves, chambers, or arteries can be malformed, absent, or abnormally placed.