BACKGROUND: Influenza virus is one of the major viral respiratory pathogens infecting human beings. OBJECTIVES: To determine the influenza A virus variants responsible for the 2006-2007 epidemic season in Corsica Island, France. STUDY DESIGN: Of 134 nasal samples of adult patients tested by culture and RT-PCR assays, 85 influenza A strains were identified; 81 (95%) were sub-typed as A/H3N2 and 4 (5%) were sub-typed as A/H1N1. RESULTS: All of the HA sequences of the A/H3N2 viruses circulating in Corsica Island appeared to be closely related to the A/Wisconsin/67/2005 vaccine strain and segregated into two sub-groups that were genetically distinct from other viruses circulating in other countries during 2006/2007. One of these sub-groups was distinguished by the substitution H156Q whereas the second demonstrated at least one of the 3 other additional mutations (R142G, L157S and K173E) common to the HA1 sequence of A/Nepal/921/2006 reference strain. Among the 14 strains of this second sub-group, 10 viral strains had been isolated from vaccinated adult patients. CONCLUSION: These findings suggest that a prospective analysis of the HA sequences of influenza isolates may allow an early detection of newly evolved variants with potential epidemiological inference.