Background: Cardiovascular diseases (CVD) and atherosclerosis are over presented in patients with systemic lupus erythematosus (SLE). Aim of the work: The aim of this study is to determine the frequency of some atherosclerosis biomarkers in SLE patients with and without CVD compared with controls. Patients and methods: 28 female SLE patients with a mean age of 30.1 ± 7.2 years and a history of CVD (SLE cases) were compared with 25 age matched SLE female patients but without a history of CVD (SLE controls) and 25 age matched population based control women (population controls). Intima, media thickness (IMT) was measured by B-mode ultrasound as a potential measure of atherosclerosis. Nontraditional biomarkers of atherosclerosis such as leptin, oxidized LDL (oxLDL) and homocysteine were also investigated. Results: SLE cases had significantly increased IMT compared with SLE controls and population controls (p < 0.001), whereas IMT of SLE controls did not differ from population controls. Compared to SLE controls, SLE cases had raised circulating levels of leptin (p < 0.001), homocysteine, dyslipidemia with raised triglycerides (p < 0.001), decreased HDL-cholesterol concentration, (p < 0.001), lupus anticoagulants (p = 0.01), and higher cumulative prednisone dose (p = 0.4). Disease duration was comparable between the two SLE groups and the blood pressure and body mass index (BMI) were similar among the 3 groups. Conclusion: A set of distinct CVD risk factors (biomarkers of atherosclerosis) separate SLE cases from SLE controls and normal population controls. If confirmed in a prospective study, they could be used to identify SLE patients at high risk of CVD in order to optimize treatment.