In Finland, the whole-cell pertussis vaccine was replaced with acellular pertussis vaccine in the national immunisation schedule in 2005. Adolescent booster vaccinations were also included in the programme. The aim of this study was to evaluate the effects of these changes on the epidemiology and strain characteristics of Bordetella pertussis. From the national register, we first analysed all the laboratory diagnosed cases during the study years in 1999-2006. The major pool of the 6876 cases was among adolescents and adults. After the change of the programme and the introduction of the adolescent boosters, a general reduction of the incidence was noticed but this might be related to the natural epidemic cycles of pertussis. Secondly, a questionnaire was sent to the families of the 517 young children (<2 years of age) with registered, laboratory confirmed pertussis diagnosed during the study years. Of these, 319 (62%) participated the study. Forty-five percents of the cases in this cohort were younger than 3 months, the age of the first pertussis immunisation in schedule. Only 4% of the children in vaccination age were totally unimmunised. Thirdly, isolates of B. pertussis were analysed and found to differ from the used whole-cell pertussis vaccine strains by their prn, ptxA and PFGE profiles. However, no significant differences were found between the strains from patients with different immunisation status or age. Despite marked changes in the virulence genes and the genomes of the circulating B. pertussis strains have occurred, the epidemiological data from the national reporting system indicates that the whole-cell and acellular vaccines still protect against pertussis, but the results stress the importance of early primary immunisations and the need for booster immunisations.