Prolonged cough occurs in a large proportion of the 2 million pilgrims who participate in the annual Hajj in Saudi Arabia. There is no unique cause for pilgrims’ respiratory involvement, but several studies suggest a high incidence of influenza as a cause of the disease. To determine influenza vaccine efficacy against respiratory disease in pilgrims, we conducted two similar cohort studies on 51100 Iranian pilgrims who had participated in the annual Hajj in the years 2003 and 2004. We calculated vaccine efficacy in these two years with the use of “1- odd’s ratio” formula and compared the results. The vaccine efficacy for prevention of influenza like illness in the year 2003 was 51% but the vaccine was not efficient in the year 2004. It was concluded that etiologic agents other than influenza virus should be considered as the cause of respiratory disease in Hajj. Bacterial infections superimposed on chronic respiratory diseases, and allergic or toxic conditions are suggested caourses for more investigation.