Heparin-induced thrombocytopenia (HIT) is an immune-mediated thrombocytopenia resulting from prior heparin exposure. It can be associated with limb- or life-threatening thrombotic events. Patients undergoing any vascular procedures including endovascular procedures that require heparin administration are at risk. There is very little reported in the literature with regards to thrombosis associated with HIT after endovascular aortic aneurysm repair. All reported cases of HIT thrombosis presented as acute arterial lower limb ischemia or deep vein thrombosis. In this report, we present a case of HIT complicated by stent graft thrombosis and bowel ischemia.