Growing number of Bordetella pertussis infections in 1997-1998 in Poland overshadowed the successful national vaccination program. This situation prompted us to investigate if this shift reflects changes in the B. pertussis population. We investigated the possible divergence in genes encoding pertussis toxin subunit 1 (PtxS1) and pertactin (P.69) in B. pertussis population strains during the period of 1960-2000. The pertussis toxin and pertactin variants (ptxS1B and prn1) were found in strains used for production of the whole-cell pertussis vaccine (WCV) production in Poland. Results of the study indicate that the ptxS1A-allele replaced the vaccine variant in 69% in the 1960s, and in 100% in 1990s, and although the prn1-allele was found in all strains from the 1960s and 1970s, after 1995 was gradually replaced by prn2 and prn4 variants. Presumably, vaccination could affect the population structure of B. pertussis in Poland and resulted in antigenic shift in both genes analyzed. Our findings may have implications for the composition of polish WCV and the currently licensed acellular pertussis vaccines.