Abstract Background The Neisseria gonorrhoeae pilE gene encodes the PilE protein, the major subunit of the Type IV pilus and a primary colonization and virulence factor. The pilE gene undergoes high-frequency diversification mainly through gene conversion from one of many pilS copies. These unique molecular processes contribute to gonococcal population diversity, facilitating immune evasion. While the process of pilin variation is understood, the diversity of pilE and pilS genes from clinical isolates is understudied. Methods We analyzed 15 186 N. gonorrhoeae genomes, including finished (n = 65) and draft (n = 15 121) genomes, in the PubMLST database to characterize pilE and pilS gene diversity. Results The finished genomes had one to nine pilS loci at conserved chromosomal locations. Only 52.13% of sequences contained a pilE gene, despite all genomes having other Type IV pilus genes. When the pilE was present, most defined conserved sequences were preserved. However, most predicted PilE protein sequences contained premature stop codons, which were found in several silent copies. Conclusions All N. gonorrhoeae strains possess the genes necessary for pilin AV; however, most genomic sequences were derived from nonpiliated variants that emerged during in vitro culture through reversible pilus phase variation and irreversible deletion of the pilE gene.