In pilgrims returning to the UK from the Hajj in 2005 and 2006, protection from PCR-confirmed influenza by influenza vaccine was estimated using verified vaccination histories from those with symptoms consistent with influenza. Of 538 patients whose nasal swabs were analysed and immunisation histories confirmed 115 (21%) were in a high-risk group for influenza; half of these (58/115) were immunised against influenza, compared with a fifth (90/423) of those not at high risk. Five percent of vaccinated 'at risk' pilgrims compared with 14% of unvaccinated (RR 0.37, 95% CI 0.1-1.4) had confirmed influenza. Rates of influenza in vaccinated and unvaccinated 'not at risk' pilgrims were similar (10% vs. 11%). Seasonal influenza vaccine was insignificantly protective against influenza in Hajj pilgrims.