Certain DNA sequences in the genome may exist either in the canonical right-handed B-duplex or in alternative non-B conformations, depending on conditions such as transcription, supercoil stress, protein binding, and so on. Analyses of breakpoint junctions at deletions, translocations, and inversions, where the sites of DNA breakage could be determined at the nucleotide level, revealed that most, if not all, of the breaks occurred within, or adjacent to, the predicted non-B conformations. These findings support a model whereby rearrangements are caused by recombination/repair processes between two distinct non-B conformations, which may reside either on the same chromosome or on two distinct chromosomes. This model was applicable to both Escherichia coli and humans, suggesting that the mechanisms involved are highly conserved.