Background Association between antiphospholipid syndrome in systemic lupus erythematosus (SLE) and valvular heart disease (VHD) is well reported, but relatively few studies have been carried out to establish the linkage between VHD and SLE itself. We aimed to investigate link between VHD and SLE and to evaluate the association of diverse factors with VHD among these patients in a large-scale population-based study. Materials and methods We used the databases of the largest state-mandated health service organization in Israel. All SLE patients were included (n = 5018) as well as their age and sex-matched controls (n = 25 090), creating a cross-sectional population-based study. Medical records of all subjects were analysed for documented VHD and the presence of antiphospholipid antibodies (aPLs). A logistic regression model was carried out to evaluate the diverse factors including SLE and aPLs as independent risk factors for VHD. Results Valvular heart disease were found to be more frequent among SLE group when compared to controls (aortic stenosis, 108% vs. 035% respectively, P < 0001; aortic insufficiency, 132% vs. 029% respectively, P < 0001; mitral stenosis, 074% vs. 021% respectively, P < 0001; mitral insufficiency, 191% vs. 039% respectively, P < 0001). Male sex, hypertension, aPLs and SLE were found to be significant independent risk factors for VHD. Conclusion All VHD are more prevalent among SLE patients when compared to controls. SLE and aPLs are independent risk factor for VHD (OR of 246 and 17, respectively). Physicians must be aware of such significant association, and routine echocardiography should be considered in SLE patients regardless of their aPL status.