At birth, a dramatic change in the circulatory pattern occurs. The lungs inflate, which lowers resistance in the lung arteries and now blood from the right ventricle preferentially flows into the lungs. The increase in blood flow into and out of the lungs increases pressure in the left atrium. This causes a one-way flap on the left side of the foramen ovale, called the septum primum, to press against the opening, effectively separating the two atria. This also further increases blood flow to the lungs as blood entering the right atrium can no longer bypass the right ventricle.

Also, within a day or two of birth, the ductus arteriosus closes off, preventing blood from the aorta to the pulmonary artery.

If the changes described above do not take place after birth, congenital heart disease may result. For example, if the ductus arteriosus remains open (or patent), heart failure may occur. Interventional and/or pharmaceutical treatments are often successful in correcting these conditions.