Background: Respiratory disorders are the most common diseases among Iranian pilgrims in Hajj. Some studies recommended flu and pneumococcal vaccines separately or in combination to reduce respiratory diseases occurrence and its morbidity. These effects are not clear in afflicted Hajj pilgrims. Objective: This is a cohort study that investigates the effects of above-mentioned vaccines each or their combination on respiratory syndromes and their consequences among Iranian pilgrims in Mecca. Method: The participants were 295 Iranian pilgrims from the beginning to the end of the journey. They were systematically observed for getting afflicted with a respiratory syndrome or not. In this study, we have assessed the effects of flu and pneumococcal vaccines on respiratory disease occurrence and on 8 clinical consequences including as: the duration of fever, duration of cough, duration of bed rest, presence of post nasal discharge and dirty sputum, the total disease length, and the number of referrals to the hospital, physician’s visits and complications. The data for this study were gathered through a questionnaire with 14 basic questions and 60 choices. This was processed using the SPSS software of 11.5 version, T- and Chi-square tests. Results: The results showed no significant correlations between the above-mentioned factors and vaccination with one or both flu and pneumovax-23 except for the duration of coughs which was significantly reduced in all cases (p < 0.01) and also decreased complications of the disease (p < 0.001). Conclusion: The study suggests the high-risk groups, should be vaccinated with combination of flu and pneumovax-23 vaccines in Hajj.