INTRODUCTION: Infective endocarditis (IE) is a life-threatening condition and a rare cause of ischemic stroke (IS). This study aimed to evaluate the utility of analyzing cerebral thrombi, obtained through endovascular thrombectomy in IS, for the pathological diagnosis of IE. PATIENTS AND METHODS: Cerebral thrombi from three groups of IS patients were compared: definite IE ( RESULTS: Median age of included patients was 73 years and 50% were females. Hematoxylin & Eosin and Grocott-Gomori Methenamine Silver stains detected microorganisms in all IE cerebral thrombi, and none in the control groups. Thrombus PCR detected relevant microorganism in n = 2/7 IE. Compared to control groups, IE thrombi were characterized by significant lower content of red blood cells (median [IQR]: IE = 7.4 [4.2-26.7], CE-I DISCUSSION: Multimodal analysis of cerebral thrombi in IS with suspected IE supports early and definite pathological diagnosis by detecting pathogens and assessing changes in thrombus composition.