Abstract Class switch recombination (CSR) produces secondary immunoglobulin isotypes and requires AID-dependent DNA deamination of intronic switch (S) regions within the immunoglobulin heavy chain gene locus. Non-canonical repair of deaminated DNA by mismatch repair (MMR) or base excision repair (BER) creates DNA breaks that permit recombination between distal S regions. ATM-dependent phosphorylation of AID at serine-38 (pS38-AID) promotes its interaction with APE1, a BER protein, suggesting that ATM regulates CSR through BER. However, pS38-AID may also play a role in MMR during CSR, although the mechanism remains unknown. To examine whether ATM modulates BER- and/or MMR-dependent CSR, ATM−/− mice were bred to mice deficient for the MMR gene MSH2. Surprisingly, the predicted Mendelian frequencies of ATM−/− MSH2−/− adult mice were not observed. To obtain ATM- and MSH2-deficient B cells, ATM was conditionally deleted on an MSH2−/− background using a floxed ATM allele [ATMF] and B cell-specific Cre recombinase expression (CD23-cre) to generate a deleted ATM allele (ATMD). As compared to the ATMD/D and MSH2−/− mice and B cells, the ATMD/D MSH2−/− mice and B cells display a reduced CSR phenotype. Interestingly, Sμ-Sγ1 junctions from ATMD/D MSH2−/− B cells that were induced to switch to IgG1 in vitro revealed a significant loss of blunt end joins and an increase in insertions as compared to wildtype, ATMD/D, or MSH2−/− B cells. This data suggests that the absence of both ATM and MSH2 blocks NHEJ and leads to inefficient end joining and the reduced CSR. We identify complementary roles for ATM and MSH2 in NHEJ and A-EJ during CSR and propose a model whereby ATM and MSH2 function cooperatively to regulate end-joining during CSR through pS38-AID. This work was supported by The National Institute on Minority Health and Health Disparities (5G12MD007603), The National Cancer Institute (2U54CA132378), and The National Institute of General Medical Sciences (1SC1GM132035-01).