Eisenmenger's syndrome arises from the persistence of the truncus arteriosus.

Failure of fusion between components of the membranous portion of the interventricular septum allows blood flow between chambers. The increased pressure and afterload on the right ventricle causes hypertrophy. The following diagram represents an oblique cut through the heart. Note that in Eisenmenger's syndrome, the division between the ascending aorta and the pulmonary artery are roughly equal. The position of the truncus directly above the VSD is referred to as an overriding truncus.

Characteristics of Eisenmenger's syndrome summarized:
- persistent truncus arteriosus
- ventricular septal defect
- left-right ventricular shunt
- right ventricle hypertrophy
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