Objectives: Bordetella pertussis is a Gram-negative coccobacillus bacterium which is the causative agent of whooping cough. In recent years, the number of whooping cough cases has been rised. This bacterium has important virulence factors such as fimbriae and pertactin. In this study, polymorphism of Serotype 2 and 3 fimbriae genes and 2 Regions of pertactin gene were surveyed. Materials & Methods: Totally, 20 B. pertussis clinical isolates were tested. DNA was extracted using the kit. Serotypes 2 and 3 fimbriae genes and pertactin Region 1 and 2 were identified using PCR method; finally, 13 samples were randomly sequenced. Findings: No mutation was observed in the pertactin Region 2. In relation to the region1 of pertactin, %77 and %23 of the strains had prn2 and prn1 alleles, respectively. In relation to fim2 gene, %70 and %30 of the strains had fim2-2 and fim1-2 alleles, respectively. Also, in relation to fim3 gene, %70 and %30 of the strains carried fim3B and fim3A alleles, respectively. Conclusion: In general, the present study results were similar to those of the previous studies conducted in Iran, but there were some differences in fim2 gene polymorphism so that the dominant allele changed from fim1-2 to fim2-2. Considering the fact that vaccine strains of Bp134 and Bp509 carry fim3A allele, which is different from the dominant circulating allele (fim3B), it is suggested that strains more similar to the dominant circulating strains should be used in designing vaccines.