Our aim was to investigate whether neurological impairment in Behcet's disease (BD) can be assessed by means of proton MRS and whether it can assist in prognosis. We used single-voxel MRS to measure metabolites in regions of normal-appearing pons, basal ganglia and periventricular white matter (PWM) in 32 patients with chronic BD patients with and without neurological deficits and 29 control subjects. Patients had significantly higher N-acetylaspartate (NAA)/creatine (Cr) and choline (Cho)/Cr ratios in the basal ganglia than the controls. The Cho/Cr ratio in the PWM was also significantly higher in the patients. MRS enabled clear discrimination of patients and controls and also revealed spectral differences between non-neuro-Behcet's disease and neuro-Behcet's disease in the basal ganglia. MRS can be used to assess brain involvement in BD even if structural changes are absent.