BACKGROUND: The seasonal influenza vaccination programme in England targets individuals over 65 years old and in clinical risk groups. METHODS: A model of influenza transmission and disease was fitted to weekly primary care consultations due to influenza in a typical pre-pandemic season (2006/2007). Different scenarios were constructed about influenza severity and how well vaccines match circulating strains to assess the impact and cost-effectiveness of the current vaccination programme. RESULTS: A well-matched vaccine may reduce the incidence of laboratory-confirmed influenza illness from 8.2% (95% range 4.3-13%) to 5.9% (95% range 2.9-9.7%), with 56-73% of this due to indirect protection. The programme is likely to be cost-effective unless both low severity and poor matching is assumed. CONCLUSION: The current seasonal influenza vaccination programme appears to substantially reduce disease burden and provides good value for money.