We compared pertussis surveillance systems of 16 European countries in the period 1998-2002. In twelve out of sixteen countries the system covered the general population. Ten countries relied on WHO case definition for surveillance of pertussis. Eleven countries applied laboratory tests, and eight of them used PCR for case confirmation. The proportion of hospitalised rates in children<1 year varied between 33.1 and 100%, while case fatality in the same age group varied between 0 and 21.3 per 1000. The adoption of WHO case definition, standardisation of laboratory diagnosis, and integration of information on deaths from alternative sources should be supported.