Transposons transfer DNA from one site on the bacterial chromosome to another site or to a plasmid. They do so by synthesizing a copy of their DNA and inserting the copy at another site in the bacterial chromosome or the plasmid. The transfer of a transposon to a plasmid and the subsequent transfer of the plasmid to another bacterium by conjugation contributes significantly to the spread of antibiotic resistance.

Transfer of DNA within bacteria also occurs by programmed rearrangements (Figure). These gene rearrangements account for many of the antigenic changes seen in Neisseria gonorrhoeae and Borrelia recurrentis, the cause of relapsing fever. A programmed rearrangement consists of the movement of a gene from a silent storage site where the gene is not expressed to an active site where transcription and translation occur. There are many silent genes that encode variants of the antigens, and the insertion of a new gene into the active site in a sequential, repeated programmed manner is the source of the consistent antigenic variation. These movements are not induced by an immune response but have the effect of allowing the organism to evade it.