Influenza A (H3N2) and influenza B viruses isolated recently in South Africa were analysed by partial nucleotide sequencing of the haemagglutinin gene to examine antigenic drift of the isolates relative to the vaccine strains. The genomic analysis of the influenza B isolates revealed a number of differences in the amino acid residues compared with those of the B/Panama/45/90 vaccine strain, and these isolates were found to be antigenically more closely related to B/Quindao/102/91. In both the 1993 and 1994 influenza A (H3N2) isolates significant drift had taken place compared with the H3N2 vaccine strains for those years, emphasizing the need for an influenza vaccine formulated specifically for the southern hemisphere.