Introduction: Despite high level of vaccination against pertussis‚ whooping cough has re-emerged as a health threat, especially in infants. This could be related to expansion of Bordetella pertussis with novel alleles for virulence factors including the pertussis toxin promoter, ptxP3. Compared to ptxp1 strains‚ ptxp3 strains produce more pertussis toxin which results in immune suppression and virulence. The main aim of this study was the determination of dominant alleles of the promoter region of the gene coding for pertussis toxin in B. pertussis isolates in Iran. Methods: In this project, we studied the allelic variations in ptxP3 .This factor was sequenced and analyzed in 35 B. pertussis isolates from Iranian patients in 2011. Biochemical tests were performed to confirm the B. pertussis isolates. Ultimately, polymerase chain reactions and sequencing were done. Results: Our results showed that the predominant allele among the strains was ptxP3. One isolated strain (i.e. ptxP1) showed different results from the other strains. Also, B. pertussis 134 and 509 as common vaccine strains used in Iran were analyzed and they were identified to be ptxP1. Conclusion: Based on our results in recent years‚ the vaccine strains and the circulating strains do not share the same alleles which could be one of the causes of pertussis resurgence in the world. ptxP is a well-known toxin of B. pertussis which is responsible for binding to the host cell and the disruption of the cellular function. In particular‚ allelic variation in ptxP may play a role in adaption of B. pertussis.