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Background: Clinical thromboembolism in Fontan patients is often a catastrophic event resulting in death and adverse long-term outcomes. The treatment of acute thromboembolic complications in these patients is very controversial.

Case Summary: We describe the use of rheolytic thrombectomy in a Fontan patient with life-threatening pulmonary embolism, employing a cerebral protection system to reduce the risk of stroke through the fenestration.

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