Intravenous central line catheters are often at risk of line-related thrombosis. We report on how the cardiopulmonary bypass strategy was tailored to the particular anatomical challenges with the use of an unconventional venous cannulation site to optimise intraoperative venous drainage, improve surgical exposure and avoid circulatory arrest in a case with a complex intracardiac thrombosis. This report also highlights the importance of assiduously monitoring the efficacy of anticoagulation therapy, especially in the context of small bowel syndrome.