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The Fontan procedure is nowadays used where a child only has a single effective ventricle, either due to defects of the heart valves (e.g. tricuspid atresia or pulmonary atresia) or an abnormality of the pumping ability of the heart (e.g. hypoplastic left heart syndrome), or has complex congenital heart disease where a bi-ventricular repair is impossible or inadvisable.

These children have a single effective ventricle supplying blood to the lungs and the body (either from birth or after an initial surgery e.g. Norwood procedure).

They are delicately balanced between inadequate blood supply to the lungs (causing cyanosis) and oversupply to the lungs (causing pulmonary edema). In addition, the single ventricle is doing nearly twice the expected amount of work (because it has to pump blood for both lungs and body). As a result, these children can have trouble gaining weight, and are also vulnerable to decompensation in the face of otherwise minor illnesses (even a common cold).

Sometimes medications (e.g. diuretics) can help them through this stage.
Therefore, when either they are large enough, or when they decompensate more than can be managed medically, these children are referred for Fontan procedure.

After Fontan, blood must flow through the lungs without being pumped by the heart. Therefore children with high pulmonary vascular resistance may not tolerate a Fontan procedure. Often cardiac catheterization is performed to check the resistance before proceeding with the surgery. (This is also the reason a Fontan procedure cannot be done immediately after birth; the pumonary vascular resistance is high in utero and takes months to drop.)

There are three different types of Fontan procedure:
- Atriopulmonary connection (the original)
- Intracardiac total cavopulmonary connection (lateral tunnel)
- Extracardiac total cavopulmonary connection

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