Arterial thrombosis in systemic lupus erythematosus (SLE) and nephrotic syndrome have been infrequently reported. A 16-year-old boy with SLE and longstanding nephrotic syndrome presented with peripheral arterial thrombosis when his lupus was at an inactive stage. He did not have antiphospholipid antibodies but had low serum antithrombin III and protein S levels. We suggest that the thrombotic event is not related to antiphospholipid antibodies but to nephrotic syndrome and possibly to acquired protein S deficiency.