To investigate the molecular events associated with B cell apoptosis, we analyzed follicular B cells from the large Peyer's patch (PP) in the sheep ileum. Over 95% of B cells generated in the ileal PP are rapidly destroyed by apoptosis. Ig V lambda sequences from apoptotic B cells were compared with sequence from B cells about to emigrate from the PP. The sequences originated from two germline genes, V lambda 5.1 and V lambda 5.3. Only V lambda 5.1 was rearranged in apoptotic cells, whereas both V lambda 5.1 and V lambda 5.3 were rearranged in B cells about to emigrate. Apoptotic B cells had evidence of increased Ig sequence diversity based on: 1) significantly greater replacement to silent mutation ratios in the complementarity determining regions, 2) the more random distribution of mutations, and 3) the lack of mutational specificity compared with the mutational bias favoring transitions and purines in B cells about to emigrate. Based on this analysis, we propose that the continual proliferation of B cells in the PP follicle might increase their affinity to local Ags. Those Ags that are sequestered in this environment might be expected to stimulate the production of B cells with such high-affinity receptors that ligation would trigger apoptosis. This could account for the deletion of B cells with specificity for self-antigens, selecting ligands as well as gut-derived food and microbial Ags. This process could contribute to the elimination of self-reactive B cells, the expansion of the antibody repertoire, and the generation of oral tolerance.