Somatic hypermutation (SHM) of antibody variable region genes is initiated in germinal center B cells during an immune response by activation-induced cytidine deaminase (AID), which converts cytosines to uracils. During accurate repair in nonmutating cells, uracil is excised by uracil DNA glycosylase (UNG), leaving abasic sites that are incised by AP endonuclease (APE) to create single-strand breaks, and the correct nucleotide is reinserted by DNA polymerase β. During SHM, for unknown reasons, repair is error prone. There are two APE homologs in mammals and, surprisingly, APE1, in contrast to its high expression in both resting and in vitro-activated splenic B cells, is expressed at very low levels in mouse germinal center B cells where SHM occurs, and APE1 haploinsufficiency has very little effect on SHM. In contrast, the less efficient homolog, APE2, is highly expressed and contributes not only to the frequency of mutations, but also to the generation of mutations at A:T base pair (bp), insertions, and deletions. In the absence of both UNG and APE2, mutations at A:T bp are dramatically reduced. Single-strand breaks generated by APE2 could provide entry points for exonuclease recruited by the mismatch repair proteins Msh2-Msh6, and the known association of APE2 with proliferating cell nuclear antigen could recruit translesion polymerases to create mutations at AIDinduced lesions and also at A:T bp. Our data provide new insight into error-prone repair of AID-induced lesions, which we propose is facilitated by down-regulation of APE1 and up-regulation of APE2 expression in germinal center B cells. D uring humoral immune responses, the recombined antibody variable [V(D)J] region genes undergo somatic hypermutation (SHM), which, after selection, greatly increases the affinity of antibodies for the activating antigen. This process occurs in germinal centers (GCs) in the spleen, lymph nodes, and Peyer's patches (PPs) and entirely depends on activation-induced cytidine deaminase (AID) (1, 2). AID initiates SHM by deamination of cytidine nucleotides in the variable region of antibody genes, converting the cytosine (dC) to uracil (dU) (1, 3, 4). Some AIDinduced dUs are excised by the ubiquitous enzyme uracil DNA glycosylase (UNG), resulting in abasic (AP) sites that can be recognized by apurinic/apyrimidinic endonuclease (APE) (4, 5). APE cleaves the DNA backbone at AP sites to form a singlestrand break (SSB) with a 3′ OH that can be extended by DNA polymerase (Pol) to replace the excised nucleotide (6). In most cells, DNA Pol β performs this extension with high fidelity, reinserting dC across from the template dG. In contrast, GC B cells undergoing SHM are rapidly proliferating, and some of the dUs are replicated over before they can be excised and are read as dT by replicative polymerases, resulting in dC to dT transition mutations. Unrepaired AP sites encountering replication lead to the nontemplated addition of any base opposite the site, causing transition and transversion mutations. However, it is not clear why dU...