Human influenza viruses are subject to continuous antigenic drift and this phenomenon poses great problems for the annual production of vaccines which should ideally be manufactured from strains closely matching the predominant strains of the coming influenza season. We have investigated the dynamics of antigenic and genetic changes in the hemagglutinins of circulating influenza A/H3N2 strains in three consecutive seasons (2002/2003 to 2004/2005) in Austria by sequence analysis of the HA1 domain and by antigenic characterization using a hemagglutination inhibition assay. Each of the three seasons was dominated by a single and different H3N2 variant, but in all cases sequencing revealed the co-circulation of a drift variant which would have been missed by conventional antigenic analysis. These emerging strains always showed already a close genetic relationship to the dominating strain of the following season. Our results underscore the value of monitoring seasonal influenza strain dynamics by sequence analysis as an instrument that can provide important and timely information on the appearance of strains with epidemiologic significance.