Divergence has been found between Bordetella pertussis vaccine strains and circulating strains. Polymorphism in pertactin (Prn) is essentially limited to region 1, which is made up of repeats. Today, the 3 most prevalent Prn variants are Prn1-3. Vaccine strains produce Prn1, whereas Prn2 is the predominant type found in circulating strains. We investigated how variation in region 1 affects the production of human serum antibodies. Individuals infected by Prn2 strains had significantly fewer antibodies to Prn1 did than those infected by Prn3 strains and those immunized with a booster dose of acellular vaccines containing Prn1. Moreover, in contrast to vaccine recipients and subjects infected by Prn3 strains, individuals infected by Prn2 strains had hardly any antibodies specific to the variable region of Prn1. These results indicate that conformational changes have occurred in the variable region of Prn, which may offer a possible explanation for the emergence of Prn2 strains in certain countries.