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Background and purpose. Risk of acute ischemic stroke has been associated with carotid artery atherosclerosis as well as with periodontal disease. We studied whether oral pathology or carotid atherosclerosis was associated with the presence and quantity of bacterial DNA in their aspirated thrombi. Methods. Thrombus aspirates and control arterial blood were taken from 71 patients (70.4% male; mean age, 67.4 years) with acute ischemic stroke. Tooth pathology was registered using CT scans. Carotid stenosis was estimated with CTA and ultrasonography. The presence of bacterial DNA from aspirated thrombi was determined using quantitative PCR. We also analyzed the presence of these bacterial DNAs in carotid endarterectomies from patients with peripheral arterial disease. Results. Bacterial DNA was found in 59 (83.1%) of the thrombus aspirates (median, 8.6‐fold). Oral streptococcal DNA was found in 56 …