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Abstract Background Autoimmune diseases, such as systemic lupus erythematosus (SLE), are associated with thrombosis and atherosclerosis. Presence of lupus anticoagulant is an independent risk factor for atherosclerotic diseases. Case presentation A 56-year-old man with past history of hypertension, and cerebral infarction was admitted to our hospital owing to acute chest pain. He was diagnosed with acute myocardial infarction based on his symptoms and electrocardiogram results, which demonstrated ST elevation in the precordial leads. Coronary angiography images revealed total occlusion at the proximal site of the left anterior descending artery. A drug-eluting stent was deployed, which successfully recovered coronary blood flow. The patient had fever of unknown cause when he was 30 years old; on admission, he presented with a low-grade fever and reddish exanthema affecting both cheeks. Based on his physical signs as well as elevated antinuclear antibodies (anti-double-stranded DNA), decreased lymphocytes, and a positive direct Coombs test, he was diagnosed with SLE. Owing to a positive lupus anticoagulant test, he was also suspected to have antiphospholipid syndrome (APS). Triple antithrombotic therapy, including dual antiplatelet therapy with aspirin and clopidogrel during coronary stenting and single anticoagulation therapy with warfarin, was initiated. Conclusions Careful diagnosis of autoimmune diseases should be performed in patients with thrombosis and atherosclerosis. Moreover, risk factors for coronary artery disease should be strictly controlled in patients with APS.