Thirty-three Neisseria gonorrhoeae isolates from 15 persons infected multiple times with the same serovar were compared using por gene sequencing, opa-typing, and arbitrarily primed-polymerase chain reaction. All three molecular techniques were more discriminatory than serotyping and identified differences between some isolates belonging to the same serovar. Although there were differences among Por sequences within some serovars, 10 of 15 subjects became reinfected with gonococci expressing identical Por proteins. Sequence analysis of por genes revealed evidence of horizontal genetic exchange and point mutations in potential surface-exposed regions during passage in the community.