The generation of a diverse antigen receptor repertoire is fundamental for the functionality of the adaptive immune system. While the V(D)J recombination process that generates the primary antigen receptor repertoire is understood in great detail, it is still unclear by which mechanism immunoglobulin (Ig) genes are further diversified by somatic hypermutation. Using mouse strains that carry a non–functional, predefined VHDHJH gene segment in their IgH locus we demonstrate DNA double–strand breaks (DSBs) in and around VHDHJH in B cells undergoing somatic hypermutation. The generation of these DSBs depends on transcriptional activity, and their distribution along the VHDHJH segment parallels that of point mutations in the hypermutation domain. Furthermore, similar to hot spots of somatic hypermutation, 50–60% of all DSBs occur preferentially at RGYW motifs. DSBs may transiently dissociate the Ig promoter from the intronic enhancer to block further transcription and to initiate an error–prone nonhomologous DSB repair pathway. In accord with this model large deletions are frequently produced, along with point mutations, in a VHDHJH segment inserted together with its promoter into the IgH locus in inverted orientation. Our data suggest that DSBs are reaction intermediates of the mechanism underlying somatic hypermutation.