Hyperhomocysteinaemia is strongly associated with increased relative risk of occlusive vascular disease, mainly of the carotid and coronary arteries. The aim of our study was to assess whether raised plasma homocysteine is a risk factor for thrombotic events in patients with systemic lupus erythematosus (SLE), a condition known to be associated with premature atherothrombotic complications. The study included 34 consecutive consenting SLE patients who were seen in the Rheumatology Unit of Al-Amiri hospital, one of the main teaching hospitals in Kuwait. Twenty consenting healthy subjects were included in the control group. Twenty-four patients were grouped as SLE without thrombosis and 10 had different types of thromboses. Vitamin B₁₂, folate, anticardiolipin antibodies (IgG and IgM), activated partial thromboplastin time (APTT) and total homocysteine level were measured for both patients and controls. A raised homocysteine concentration was defined as plasma homocysteine level above 9.4 mmol/l. Hyperhomocysteinaemia was found in 21 (61.8%) SLE patients. Low levels of folate and vitamin B₁₂ were significantly associated with high concentrations of plasma homocysteine (r = −0.35 and −0.39, respectively, P<0.01). SLE patients with elevated homocysteine concentration have a threefold increase in odds ratio of thrombotic events after adjusting for other risk factors (male sex, shortened APTT, treatment with prednisone, low folate and vitamin B₁₂ levels). We concluded that homocysteine is an independent risk factor for thrombosis in patients with SLE and is potentially modifiable.