Cerebral atrophy has been described to occur in systemic lupus erythematosus (SLE) with variable frequency. The aim of this study was to determine white and gray matter abnormalities in brain magnetic resonance imaging (MRI) of patients with SLE and to determine if these abnormalities progress over a one-year period. Seventy-five patients with SLE and 44 healthy age and sex-matched controls were enrolled in this study. T1-weighted volumetric images were used for voxel based morphometry (VBM) analyses. SLE patients exhibited a significant reduction in white matter and gray matter volume compared to controls (p=0.001). Follow-up images, after an average interval of 19 months, revealed a progressive white matter and gray matter atrophy (p=0.001). Reduced white and gray matter volume was associated with disease duration and the presence of antiphospholipid antibodies. Patients with severe cognitive impairment had a more pronounced white and gray matter reduction than patients with moderate cognitive impairment. Total corticosteroid dose was associated with gray matter reduction and not with white matter loss in SLE patients. We concluded that brain tissue loss associated with SLE is significant and progresses over a relatively short period of time. Disease duration, the presence of antiphospholipid antibodies and cognitive impairment were associated with white and gray matter loss. Corticosteroid was associated only with gray matter atrophy.