Influenza A viruses are characterized by a unique genome structure, causing genetic instability, especially to the genes of haemagglutinin and neuraminidase. The objectives of this research was molecular and phylogenetic analysis of influenza A(H3N2) strains that circulated in Northern Greece since 2004, particularly the identification of sequence variations and the comparison of circulating viruses with vaccine strains. Since 2004 in Northern Greece, a total of 216 clinical samples were positive for influenza virus infections, of which 83 (38.4%) were attributed to influenza A(H3N2). Molecular analysis of the HA genes of 23 isolates showed that all circulating strains had variations at antigenic sites. Receptor binding sites were conserved in 2004-2005 and 2005-2006 strains whereas a variation was observed in all 2006-2007 strains (H195Y). Furthermore, alternative amino acids for sialic acid receptor binding sites were observed in most of the 2004-2006 isolates. Some amino acid substitutions were also observed at the neuraminidase sequences, which however had no effect on the antigenicity of the viruses. Phylogenetic analysis of each year's circulating strains revealed a relatively low match with the vaccine strains A/Fujian/411/02 and A/California/7/04 for 2004-2005 and 2005-2006, respectively, whereas most 2006-2007 isolates match with the vaccine strain, A/Wisconsin/67/05. This year, unique variations were observed at antigenic and glycosylation sites of A/Serres/77/07-like stains. Constant surveillance of yearly variations is of great importance, so that vaccine strains can be evaluated.