The emergence of respiratory diseases, i.e., severe acute respiratory syndrome (SARS) epidemic in 2003, H1N1 influenza epidemic in 2011 and Middle East respiratory syndrome (MERS) outbreak, reiterated the significance of ventilation in buildings. The role of ventilation in removing exhaled airborne bio-aerosols and preventing cross infections has been multidisciplinary extensively studied after the SARS outbreak in 2003. The characteristics of droplet-borne, short-range airborne and long-range airborne transmission of infectious diseases were identified. Increasing ventilation rate can effectively reduce the risk of long-range airborne transmission, while it may be of little useful in preventing the droplet-borne transmission. To maintain the airflow direction from clean cubicles to dirty cubicles is an effective way to prevent the cross infection between cubicles, which is widely used in hospital isolation rooms. Field measurements showed that wrong air flow direction was due to poor construction quality or maintenance. The impacts of different airflow patterns on removing large droplets and fine droplet nuclei were discussed. Some new concepts in general ventilation systems and local personalized equipment were also introduced. This review updates current knowledge of the airborne transmission of pathogens and the improvement of ventilation efficiency concerning the infection prevention.