The aim of this study was to determine the clinical implications of migraine in systemic lupus erythematosus (SLE) using the cumulative organ damage scores (SLICC-DI). Eighty SLE, 40 rheumatoid arthritis (RA) patients and 40 controls (non SLE, nor RA out-patients), all women, were included. Migraine was defined according to the International Headache Society (IHS) criteria for neuropsychiatric SLE. Disease activity was measured by MEX-SLEDAI and cumulative organ damage by SLICC-DI. Statistics were obtained by Chi-square and Fischer's exact tests. anova was used for comparing means. Migraine was identified in 42.5% of SLE patients, compared to 12.5% of RA patients (P < 0.05) and 10.0% (P < 0.05) in the control group. In the SLE group, a significant association between migraine and Raynaud's phenomenon (P = 0.003, OR = 10.1; 95%CI 2.9-35) and antiphospholipid antibodies (P = 0.0012; OR = 7.5; 95%CI 2.5-22.9) was noted. SLE patients with active migraine had higher MEX-SLEDAI scores than SLE patients without migraine. SLE patients with past history of migraine had significantly higher SLICC scores than SLE patients without migraine. History of migraine was associated with greater organ damage. Active migraine was associated with higher disease activity, antiphospholipid antibodies and worsening of Raynaud's phenomenon. The increased cumulative organ damage in SLE patients with past history of migraine justifies the routine evaluation of migraine in clinical practice.