Abstract Systemic lupus erythematosus is a chronic systemic autoimmune disease, often associated with severe infection. A female patient was referred for surgical treatment of infective endocarditis after being treated for systemic lupus erythematosus and lupus nephritis. She developed symptoms of left axillary artery occlusion before heart operation. Bulky fungal hyphae were noted on pathological examination of the surgically removed thrombi. The patient had an uncomplicated recovery after receiving high doses of antibiotics and subsequent mitral valve replacement. Either infective endocarditis or fungal thrombi may be secondary to systemic lupus erythematosus and impaired renal function.