The first sign of influenza activity in the Netherlands during the 2005-2006 influenza season was the isolation of influenza viruses in the last week of 2005. From Week 1 of 2006 onwards, an increase in clinical influenza activity was also observed that did not return to baseline levels until Week 15. Two waves of influenza activity were observed with peak incidences of 13.8 and 9.8 influenza-like illnesses per 10,000 inhabitants on Weeks 7 and 12, respectively. The first wave of influenza was caused primarily by influenza B viruses, whereas the second wave was caused predominantly by influenza A/H3N2 viruses. The influenza B viruses appeared to belong to two different phylogenetic lineages and were antigenically distinguishable from the vaccine strain. The isolated influenza A/H3N2 viruses were closely related to the vaccine strain for this subtype and only minor antigenic differences with the vaccine strain were observed for a limited number of isolates. Only a small number of influenza A/H1N1 viruses were isolated, which all closely resembled the H1N1 vaccine strain. For the 2006-2007 influenza season, the World Health Organization has recommended the following vaccine composition: A/Wisconsin/67/05 (H3N2), A/New Caledonia/20/99 (H1N1) and B/Malaysia/2506/05.