The accumulation of B lymphocyte clones in the cerebrospinal fluid (CSF) of patients with multiple sclerosis (MS) and patients with other neurological disorders was investigated using PCR technologies. Oligoclonal B cell accumulations were detected in 10 of 10 MS patients, but only in 3 of 10 of the patients with other neurological disorders. Analyses of the Ig V (D) J sequences on the CSF from MS patients disclosed that V H 3 and V H 4 genes were extensively mutated compared with germline sequences. Moreover, a substantial proportion of the molecular clones analyzed shared the same third CDR of the H chain variable region gene (HCDR3) and the same V H genes, albeit with different numbers and locations of point mutations, thus indicating an ongoing process of intraclonal diversification. A larger number of clonally related V H sequences could be obtained by using a V H 3 gene-specific PCR so that genealogical trees depicting the process of diversification could be drawn. Analyses of the Ig V (D) J from the CSF of a patient with viral meningitis and oligoclonal B cell accumulations revealed that V H 3 genes were extensively mutated. However, no intraclonal diversification could be observed even using V H 3 gene-specific PCR methodologies. Clone-specific PCR and sequencing was used to detect the V (D) J found in the CSF of one MS patient in the PBL of the same patient. Only 1/3 of the V (D) J sequences investigated could be demonstrated in the PBL, indicating that the V (D) J genes utilized by B cells in the CSF are much less represented in the PBL. Collectively, the data suggest that in MS there is a compartmentalized clonal expansion.