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Abstract Objective To study the influence of polyvascular atherothrombotic disease on stroke patient prognosis, its relation with inflammatory markers, and to analyze the progression of atherothrombotic disease. Methods MITICO is a multi-centered prospective observational study recruiting non-anticoagulated ischemic stroke patients. Blood samples were obtained at baseline and at one year follow-up for determination of high sensitivity C reactive protein (hs-CRP), interleukin 6 (IL-6), intercellular adhesion molecule 1 (ICAM-1), vascular cell adhesion molecule 1 (VCAM-1), matrix metalloproteinase 9 (MMP-9), and cellular fibronectin (c-Fn). Patients with polyvascular atherothrombotic disease were considered when presented a history of angina–myocardial infarction, intermittent claudication or ischemic limbs-amputation at inclusion. Results The sample consisted of 863 patients, 121 of them considered as polyvascular atherothrombotic disease (14.02%). Recurrence and vascular death were higher in patients with polyvascular atherothrombotic disease, as compared to patients with monovascular atherothrombotic disease (19.8% vs. 12.4%, p = 0.022). Baseline plasma levels of IL-6 and VCAM-1 were higher in patients with polyvascular atherothrombotic disease. IL-6 and VCAM-1 levels were independently associated with a new vascular episode/vascular death. This association was stronger in the group of patients with polyvascular atherothrombotic disease. Baseline levels of IL-6, VCAM-1 and c-Fn were significantly higher in patients who developed progression of atherothrombotic disease. The increase from baseline in MMP-9 and c-Fn levels after one year follow-up was associated to progression of atherothrombotic disease. Conclusions Stroke patients with polyvascular atherothrombotic disease showed higher rates of vascular recurrence and a stronger association with inflammatory markers. Progression of atherothrombotic disease was associated with inflammatory markers.