[8] It is performed in children born with congenital heart disease without two functional ventricles and an effective parallel blood flow circuit.

This stage generally involves combining the pulmonary artery and aorta to form a larger vessel for blood to get to the body.

[13] The inferior vena cava (IVC), which carries blood returning from the lower body, continues to connect to the right atrium.

[14][12] The third stage is called the Fontan-Kreutzer procedure which involves redirecting the blood from the inferior vena cava to the lungs.

This improves the lower than normal oxygen levels and results in one functional ventricle that is responsible for supplying blood to the rest of the body.

This is also the reason a Fontan procedure cannot be done immediately after birth; the pulmonary vascular resistance is high in utero and takes months to drop.

[citation needed] In the short term, children can have trouble with pleural effusions (fluid building up around the lungs).

[15] Chronic venous hypertension from the stasis and lowered cardiac output are assumed to be at the root of lymphatic complications such as chylothorax, protein losing enteropathy and plastic bronchitis.

The Fontan procedure is palliative — not curative — but more than 80% of the cases can result in normal or near-normal growth, development, exercise tolerance, and good quality of life.

[19] However, 10% or more of patients may eventually require heart transplantation,[20] and given the long-term consequences of chronic venous hypertension and insidious organ damage, freedom from morbidity is unlikely in the long term.

This is attributed to the circulatory changes in blood flow as well as possible exposure to nephrotoxic medications, iodine contrast agents, and long term cyanotic and ischemic nephropathy.

Pregnancy has historically been discouraged in Fontan patients due to high rates of miscarriage, cardiovascular compromise, or increased mortality.

However, improvements of the Fontan operation have resulted in pregnancies with lower incidence of heart and vascular compromise in the mother.

[26] In an attempt to improve this, Fontan was engaged in research between 1964 and 1966 endeavouring to fully redirect flow from the superior and inferior vena cavae to the pulmonary artery.

[27] His initial attempts in dogs were unsuccessful and all experimental animals died within a few hours; however, despite these failures, he successfully performed this operation in a young woman with tricuspid atresia in 1968 with Dr. Eugene Baudet.