There is a lack of reported studies on how the long duration wearing of N95 respirators or surgical facemasks will affect the upper airway functions. Considering the frequency of mask wearing especially in hospitals and during an outbreak of influenza, it is essential to have such data documented. Therefore, the current study is to establish the effect of long duration wearing of N95 and surgical facemasks on upper airway functions. 47 staffs of National University Hospital Singapore in 2013 were recruited. Each of the volunteers wore both N95 respirator and surgical facemask for 3 hours on two different days. During the period of mask wearing, relative airflow rates were recorded. Smell function test was carried out before and after mask wearing. The results show that no significant change of smell test score was found after removal of both the two types of masks. With N95 respirator, more air was breathed into the upper airways compared to surgical facemask.