Neisseria gonorrhoeae and Neisseria meningitidis encode several diversity-generating systems that consistently yield mixed-population phenotypes. I will present a historical review and the current understanding of the mechanisms and phenotypes resulting from the pilin antigenic variation system. I will describe fundamental studies demonstrating that this complex diversity-generating system produces several pilus-associated phenotypes that require conserved recombination and repair factors, diploid chromosomes, an alternative DNA structure, a small non-coding RNA, and the activity of two paralogous restriction-modification modules.