Clinical isolates of Bordetella pertussis collected during the year 2004 (n=153) in eight European countries, Denmark, Finland, France, Germany, The Netherlands, Poland, Sweden, and UK, were analyzed by Pulsed-Field Gel Electrophoresis (PFGE) and compared with isolates from 1999 (n=102). The 255 isolates produced 59 distinct PFGE profiles. Among the 153 isolates from 2004, 36 profiles were found, while within the 102 isolates from 1999, 33 profiles were detected. One PFGE profile, BpSR11, was dominant (30%-50%) in all countries except Denmark (10%) and Poland (0%). In comparison with 1999 there was an increase in Finland in 2004 from 5% to 40% coinciding with a major incidence peak. Some other PFGE profiles seemed to be associated with limited dissemination. Poland was the only country in which the most common actual European PFGE profiles were not found. In a dendrogram analysis all common PFGE profiles were identified within PFGE Group IV and BpSR11 clustered together with PFGE sub-Group IVbeta. Compared with 1999, PFGE Group V representative for pertactin variant prn3 strains, had disappeared and a new cluster was seen. In conclusion some PFGE profiles, as BpSR11, evidently have a higher capacity to spread suggesting increased fitness to the present immunological environment. It is therefore of major interest to continue with surveillance programs of B. pertussis isolates as both waning vaccine-derived immunity and strain variation may play a role in the persistence of pertussis.