Although the changes that occur in Ig V region genes during a B lymphocyte's response to antigen usually result from point mutations, nucleotide insertion and deletion also alter gene sequence. We identified nucleotide insertions and deletions (3 to 12 bp) at a frequency of 1.34%, in Ig V gene cDNA from B lymphocytes residing in the synovial tissues of patients with rheumatoid arthritis. Because the added or lost nucleotides occurred in multiples of 3, they maintained the original reading frame and coded a potentially intact receptor. These V gene modifications were generated somatically, because they were identified in the original cDNA by HCDR3-specific polymerase chain reaction and were not found in other B cells using the same VH genes. Insertions and deletions were detected only in IgG+ and IgA+ transcripts, which exhibited 3 times more point mutations than IgM+ transcripts. In addition, they were usually found in the complementarity determining region, typical targets of somatic mutation. The occurrence of insertion/ deletion in isotype-switched cDNA with higher numbers of V gene mutations that localized to hot spots for V gene mutation suggests that these diversification events were related to the somatic hypermutation process. In support of this, an AGY hot spot motif and a short stretch of DNA similar in sequence to the inserted or deleted segments could be found next to the insertions/deletions, suggesting that these modifications arose from DNA duplication following DNA stand breaks. Thus, nucleotide insertion/deletion can lead to B-cell receptor diversification in B lymphocytes that clonally expand in synovial tissues of patients with rheumatoid arthritis.