The ability of influenza vaccination to provide cross-protection against heterovariant influenza strains was evaluated in a double-blind, randomized, trial in north-east Italy during the winter of 2005-2006. Of 238 adult subjects with underlying chronic diseases, 120 received MF59-adjuvanted subunit vaccine (Sub/MF59) and 118 received a conventional subunit vaccine (Subunit). Immunogenicity was measured for A/H3N2 and B influenza strains against both the homologous vaccine strains (A/New York/55/2004 and B/Jiangsu/10/2003), and the heterovariant strains recommended for the 2006-2007 season (A/Wisconsin/67/2005 and B/Malaysia/2506/2004). Although both vaccines conferred serological protection against the homologous vaccine strains and the 2006-2007 heterovariant A/H3N2 strain for a majority of subjects, the antibody response was highest in the Sub/MF59 vaccine group. For example, MF59-adjuvanted vaccination conferred significantly greater (P = 0.002) protection against the heterovariant A/H3N2 strain than the conventional subunit vaccine (79.2% vs. 61.0% of subjects, respectively). In conclusion, these results demonstrate that protection provided by influenza vaccination in adults affected by chronic diseases is lower against heterovariant strains than for homologous strains. However, addition of MF59 adjuvant to a subunit vaccine enhances immunogenicity against the A/H3N2 heterovariant strain, conferring broader protection than a conventional subunit vaccine in this population, who are at higher risk of influenza-related complications.