The primary immunoglobulin (Ig) repertoire is further diversified during secondary Ig diversification in germinal centre B cells. The secondary Ig diversification via somatic hypermutation and class switch recombination in humans and mice or by Ig gene conversion in some farm animals like chickens is based on the induction of DNA damage by activation-induced cytidine deaminase (AID), an enzyme that deaminates cytidine to uracil. These DNA lesions can either be repaired in an error-prone mode in the Ig loci or in an error-free manner, which is favoured in other cellular genes. However, the molecular mechanism of this differential repair fidelity is unknown to date. Maintenance of the integrity of the entire genome is essential for cancer prevention and activation of two different checkpoint signalling axes plays an important role in triggering cell cycle arrest and improved DNA repair. In case of long single stranded regions as a result of stalled replication forks or single strand breaks, ATR is activated, which phosphorylates the checkpoint kinase 1 (Chk1). On the other hand, DNA double strand breaks activate ATM, which phosphorylates the checkpoint kinase 2 (Chk2). Given the extensive DNA damage caused by AID during Ig diversification, activation of checkpoint control is likely, but not much is known about the effects of checkpoint signalling on secondary Ig diversification processes. In this work, we could show that the two checkpoint kinases are involved and oppose each other in the regulation of somatic hypermutation, Ig gene conversion and class switch recombination. Our results suggest that Ig diversification depends on a highly regulated interplay of the two checkpoint kinases, as Chk2 is required for efficient somatic hypermutation and class switch recombination, while Chk1 activity may contribute to the prevention of B cell lymphomas.