Because genetic predisposition to atherothrombosis in systemic lupus erythematosus (SLE) remains to be determined, the most common genetic prothrombotic factors, prothrombin G20210A and factor V Leiden mutations, were studied. Seventy-four SLE patients with vascular ischemia (SLE cases) were studied and stratified into myocardial infarction and/or cerebrovascular accident subgroup (MI/CVA), and coronary heart disease subgroup without overt arterial thrombotic events (CHD). Seventy-one SLE patients without atherothrombosis were investigated as SLE controls. Factor V Leiden was detected in six cases (five in MI/CVA, one in CHD group) and three controls (OR 2.00, 95%CI 0.48-8.32). Two cases (both CHD patients) had prothrombin G20210A mutation vs. three controls (OR 0.63, 95%CI 0.1-3.88). Anticardiolipin antibodies (aCL) were increased in cases vs. controls (39/74 vs. 27/71); however, this was not statistically significant (OR 1.82, 95%CI 0.94-3.52). Neither univariate nor multivariate analysis indicated that investigated mutations are risk factors for atherothrombosis in SLE cases, MI/CVA, or CHD subgroups. Overall, disease activity was the strongest risk factor for atherothrombosis (p=0.0014) in SLE cases. Combination of disease activity+gender was the best predictor of atherothrombotic process (p=0.00045) in this cohort. In MI/CVA subgroup, disease activity was the only predictor (p=0.0058). In CHD patients, the best predictive value was conferred by combination of hypertension+gender+disease activity (p=0.00077). No other investigated risk factor (including aCL) conferred an increased risk individually or potentiated the other risk factors. The results deny the role of investigated mutations in atherothrombosis in SLE, but they underscore the importance of disease activity (i.e., ongoing inflammation) in pathogenesis of atherosclerosis and arterial thrombosis.