The present study was performed in order to confirm the diagnostic value of isoelectrofocusing (IEF) in a large multiple sclerosis (MS) cohort and to evaluate the various neurological diseases probably to present a similar IEF profile. The cerebrospinal fluid (CSF) of 1292 patients with neurological diseases was studied by IEF. After a follow-up of 2-36 months, we only included patients with a definite MS or confirmed diagnosis of other neurological diseases (OND). MS was diagnosed in 407 patients and OND in 593 patients. For patients in whom three or more oligoclonal bands (OCB) were detected, IEF results showed a sensitivity of 85% and a specificity of 92% for the diagnosis of MS. The positive and negative predictive values were 86.5 and 90%, respectively. Inflammatory and infectious disorders of the central nervous system represented the main affections associated with OCB, including human immunodeficiency virus encephalitis, Lyme disease and less frequently Sjogren syndrome. Furthermore, when OCB were observed, 10 or more bands were more frequently found in MS than in OND (P < 0.0001). IEF of the CSF is a reliable method for the diagnosis of MS. The absolute number of bands may help to discriminate between MS and OND.