Bordetella pertussis strains demonstrate polymorphism in toxin subunit S1 (PT S1) and pertactin (Prn), which belong to major protective antigens of the pathogen. Changes in the distribution of particular alleles of ptxS1 and prn genes in local B. pertussis populations have been proposed as possible factors influencing the vaccination effectiveness. We have developed a new methodology for the identification of the alleles, which eliminates the necessity of DNA sequencing. The approach is based on the evaluation of the number of sequence repeats and detection of specific nucleotides at polymorphic sites of the genes, and utilizes products of their full or partial PCR amplification. The approach is available for a laboratory with standard equipment. The total conformity of the strategy with the DNA sequencing-based approach was proved on the full set of reference strains and a group of Polish clinical isolates. The new methodology was used to investigate a collection of 120 Polish B. pertussis strains isolated from the 1960s to 2001. Similarly to findings from other countries and to earlier Polish data, the tendency to change the vaccine types of PT S1 and Prn by the antigenically different ones was observed.