To evaluate the role of anticoagulation therapy in carotid stenting with filter devices, we compared the activated clotting times (ACT) to angiographic filter patency and to the materials found inside the filters. 29 endovascular treatments with filter cerebral protection in 27 patients affected by symptomatic internal carotid stenosis > 70% were considered. Angiographic findings, ACT and histopathologic specimens were recorded and statistically correlated. Satisfactory dilatation of the stenosis was always achieved with a complication rate of 3%. During the procedure nine filters caused temporary flow impairment. Histopathologic examination demonstrated material inside the filters in 86% of cases but this material was fibrin alone in 38% and plaque debris in 48%. Significant statistical correlation (p = 0.009) was found between low activated clotting time and occlusion of the filter. Distal protection filters can collect plaque fragments occurring during carotid stenting. A significant proportion of the debris found in the filters consisted of thrombotic material. Monitoring of heparin anticoagulation is recommended to prevent filter occlusion.