Bordetella pertussis is a Gram-negative bacterium that causes pertussis or whooping cough in humans. The incidence of pertussis has increased in young infants, adolescents and adults in many countries where the vaccination against pertussis has been used extensively. Marked changes have been found in the B. pertussis population and differences have been observed between vaccine strains and circulating isolates. Moreover, clonal expansion of certain B. pertussis strains has been associated with the recent epidemics of pertussis in several European countries. In this review, we present data on strain variation and evolution of B. pertussis in different vaccinated populations and summarize the common methods for typing of B. pertussis and their relative discriminatory power.