Despite the increasing use of embolic protection systems (EPS) for carotid stenting, their intrinsic in vivo thrombogenicity remains unknown. We studied three different types of EPS (n = 24) deployed in the carotid arteries of pigs in which pools of platelets and fibrinogen were labelled with (111)In and (125)I. The amount of clot deposition seen on photography was also scored using a qualitative scale. EPS made of fabric nets under normal flow conditions were 5-6 and 15-16 times more thrombogenic (for both platelet (P=.04) and fibrin (P=.007)) than Nitinol mesh nets. Clot deposition on Nitinol mesh nets was more abundant under flow arrest than under normal flow conditions (P=.018). EPS differ in intrinsic thrombogenicity, a characteristic of the material that could be investigated in pre-clinical studies designed to optimize devices.