Background The histologic features of thrombus may differ according to the stroke subtypes. However, in acute reperfusion therapy, fibrin-specific thrombolytics are used based on the assumption that all thrombi are alike. Aims The histologic characteristics of thrombi were compared between patients with different stroke etiologies. Methods Between April 2010 and March 2012, we analyzed thrombi retrieved from acute stroke patients during mechanical thrombectomy. All thrombi were analyzed using component-specific stains such as Martius scarlet blue for fibrins and immunostaining with CD42b antibody for platelets. The stroke subtypes were determined based on the Trial of ORG 10172 in Acute Stroke Treatment classification. Results Among 36 patients, 22 were diagnosed with cardioembolism, 8 with atherothrombosis, and 6 with undetermined etiology. In arteriogenic thrombi, red blood cells were most abundant (56.9 ± 12.2%), and the platelets covered the fibrin layers or were localized at the edge or periphery of the thrombus. In cardiogenic thrombi, fibrin was most abundant (39.5 ± 13.5%), and platelets were clustered within the rich fibrin. Red blood cells proportion was greater in arteriogenic thrombi than in cardiogenic thrombi ( p Conclusions Acute thrombi showed different histologic features according to the stroke etiology. The distribution of platelets and proportion of red blood cells and fibrin were major distinguishing factors between stroke subtypes.