Ig heavy chain class switch recombination (CSR) involves a recombination͞deletion mechanism that exchanges the expressed C H gene with a downstream CH gene. CSR is mediated by highly repetitive switch (S) region sequences and requires the activationinduced deaminase (AID). The S region 5 of the C gene (S ) can undergo high-frequency internal deletions in normal B cells and B cell lines activated for CSR, although the relationship of these deletions and CSR has not been elucidated. In this study, we introduced constitutively transcribed S or S␥2b regions into a pro-B cell line that can be activated for AID expression, CSR, and endogenous S deletions. We find that randomly integrated S region transcription units in these cells also undergo increased levels of internal rearrangements after cellular activation, indicating that the deletion process is independent of location within the Ig heavy chain locus and potentially AID-promoted. To test the latter issue, we generated hybridomas from wild-type and AIDdeficient activated B cells and assayed them for internal S deletions and S region mutations. These studies demonstrated that efficient intra-S region recombination depends on AID expression and that internal S region deletions are accompanied by frequent mutations, indicating that most S region deletions occur by the same mechanism as CSR.T he genes that encode the Ig heavy chain (IgH) and light chain (IgL) variable regions are assembled from component V, D, and J segments during early B cell development by the sitespecific V(D)J recombination reaction (reviewed in ref. 1). Subsequently, in activated mature B cells, the exons that encode the first IgH constant region expressed during development (C ) can be replaced with one of a set of downstream C H exons via a process referred to as IgH class switch recombination (CSR). CSR allows the C H -encoded effector portion of an Ig molecule to be replaced, while preserving the antigen-binding variable region (reviewed in ref. 2). CSR involves a recombination͞deletion process that generally occurs between large, repetitive switch (S) region sequences that lie just upstream to all C H exons that undergo CSR. In this context, the C H exons are organized 5Ј-V(D)J-S C -C␦-S␥3C␥3-S␥1C␥1-S␥2bC␥2b-S␥3C␥3-S C -S␣C␣-3Ј. Thus, switching from IgM to another IgH isotype involves a recombination event between the S and downstream S regions with deletion of all intervening DNA. S regions range from 1 to 10 kb in length and consist of repetitive units based on pentamers (S , S , and S␣) or 49-bp repeats (S␥3, S␥1, S␥2b, and S␥2a). With respect to given S regions, CSR junctions occur throughout the S region and occasionally in sequences just outside (3, 4). An additional genomic alteration process in mature B cells, referred to as somatic mutation (SM), introduces mutations into the IgH and IgL variable regions in the context of an antigenic response (reviewed in refs. 5 and 6).CSR can be induced in vitro by stimulating splenic B cells with an activator [e.g., anti-CD40 or lipopolysacch...