The detection of intrathecal IgA synthesis (IAS) in multiple sclerosis (MS) could be underestimated. To assess it, we develop a highly sensitive assay based on isoelectric focusing (IEF). 151 MS patients and 53 controls with different neurological diseases were recruited. IgA concentration was analyzed using a newly developed in house ELISA. IgA oligoclonal bands to detect IAS were determined by IEF. Most individuals showed an IgA concentration within normal range in serum samples (90.69%) but 31.37% of individuals had a IgA concentration below the normal range in the cerebrospinal fluid (CSF). No significant differences were observed between MS and control groups, neither in CSF nor in serum. The new IEF was more sensitive than those previously described (0.01 mg/dl of IgA), and clearly identified patients with and without IAS, that was not related with IgA concentration. Using IEF, MS patients showed higher percentage of IAS-IEF (43.00%) than the control group (16.98) (p = 0.001). The incidence was especially higher in patients with clinically isolated syndrome (66.00%). The new IFE demonstrated a higher percentage of IAS in MS patients than assumed in the past. The presence of IAS-IEF in MS is higher than in other neurological diseases.