Estimates of influenza vaccine effectiveness have mostly been derived from nonrandomized studies and therefore are potentially confounded. The aim of the current study was to estimate influenza vaccine effectiveness in preventing mortality among the elderly, taking both measured and unmeasured confounding into account. Information on patients aged >or=65 yrs from the computerised Utrecht General Practitioner database on eight influenza epidemic periods and summer periods was pooled to estimate influenza vaccine effectiveness in preventing mortality. Summer periods (during which no effect of vaccination was expected) were used as a reference to control for unmeasured confounding in epidemic periods. After adjustment for measured confounders using multivariable regression analysis, propensity score matching and propensity score regression analysis, influenza vaccination reduced mortality risk (odds ratios (ORs) 0.58 (95% confidence interval (CI) 0.46-0.72), 0.56 (95% CI 0.44-0.71) and 0.56 (95% CI 0.45-0.69), respectively). After additional adjustment for unmeasured confounding (as observed during summer periods), the association between influenza vaccination and mortality risk decreased (OR 0.69 (95% CI 0.52-0.92)). We conclude that after state-of-the-art adjustment for typical confounders such as age, sex and comorbidity status, unmeasured confounding still biased estimates of influenza vaccine effectiveness. After taking unmeasured confounding into account, influenza vaccination is still associated with substantial reduction in mortality risk.