Phase and antigenic variation of pilin expression in Neisseria gonorrhoeae result from recombination events in which variant sequences from one of the silent loci (pilS) are transferred to the expression locus (pilE). Such rearrangements were originally thought to be gene conversions, but findings showing that phase variation is partially inhibited by DNase I, that piliated (P+) cells are highly competent for DNA uptake and that gonococci readily undergo autolysis in culture, led to the suggestion that pilin variation occurs through transformation by exogenous DNA. We have developed a simple method for the selection of non-piliated (P-) cells and have evaluated naturally occurring P+ to P- transitions. Two primary pathways of pilin variation can be distinguished--transformation-mediated recombination, which is influenced by culture conditions and inhibited by DNase I, and intragenomic reciprocal recombination, which is unaffected by DNase I. Furthermore, we demonstrate that both piliated and revertible P- cells are competent for DNA uptake, an essential prerequisite of the first pathway.