Our objective was to investigate axonal dysfunction in patients with systemic lupus erythematosus (SLE) using proton magnetic resonance spectroscopy (1H-MRS). We studied prospectively 90 SLE patients (mean age of 32.5 years) and 23 normal volunteers (mean age of 33.8 years). We performed single voxel proton MRS using point resolved spectroscopy sequence over the superior-posterior region of the corpus callosum. We measured signals from N-acetyl compounds [N-acetylaspartate (NAA)] at 2.01 p.p.m., choline-based compounds (Cho) at 3.2 p.p.m. and creatine and phosphocreatine containing compounds (Cr) at 3.0 p.p.m. and determined NAA/Cr ratios. After 12 months, MRI and MRS were repeated in 50 patients and 9 volunteers. Patients were divided according to disease activity (measured by SLE disease activity index) during initial and follow-up MRS. We performed paired t-test and ANOVA with Tukey's post hoc comparisons to evaluate group differences. At study entry, 29 patients had active SLE with involvement of central nervous system (CNS) and 28 patients had active SLE without CNS manifestations. A total of 14 patients had inactive SLE with past CNS presentation, and 19 had inactive SLE without history of CNS involvement. NAA/Cr ratios were significant lower in patients with active SLE, independently of CNS involvement, when compared with patients with inactive SLE (P = 0.005) and controls (P = 0.01). We observed a significant increase in NAA/Cr ratio in 15 patients who had active SLE at initial MRS and inactive SLE at follow-up (P = 0.04). In 10 patients with active SLE both at initial and at follow-up MRS we observed a reduction in NAA/Cr ratio (P = 0.02). By contrast, there was a significant reduction of NAA/Cr ratio in 15 patients who had inactive SLE at initial MRS and active SLE at follow-up (P = 0.001). In 10 patients with inactive SLE both at initial and at follow-up MRS NAA/Cr ratio did not change (P = 0.2). This study shows evidence of axonal dysfunction in patients with active SLE, independently of CNS manifestations that may be reversible, at least in part, during periods of inactivity of disease.