High exposure risk to various infectious agents in health care facilities is of special concern, especially to airborne and droplet-borne respiratory diseases. We conducted a study to monitor indoor air quality and essential infectious aerosols (including culturable fungi, culturable bacteria and influenza A virus) in two hospitals in Taipei, Taiwan. A questionnaire survey was used to evaluate the relationships between employees’ health and measured indoor environmental factors. Our environmental monitoring was carried out in the crowded areas of study hospitals and the departments with high concentrations of infectious aerosols. The sampling sites included main lobby, emergency department, outpatient departments (internal medicine, pediatrics, neonatology, E.N.T, infectious disease, family medicine) and wards (internal medicine and pediatrics). Structured questionnaires were administered to the participants concurrently with environmental sampling and were collected after being completed. According to our results, the concentrations of total culturable fungi were 148 CFU/m3 in hospital A and 44 CFU/m3 in hospital B; the concentrations of total culturable bacteria were 476 CFU/m3 in hospital A and 399 CFU/m3 in hospital B. Mean concentrations of airborne fungi and bacteria were both highest in the main lobbies. In our study hospitals, the predominant fungi genera were non-Sporulating Fungi, Penicillium, Cladosporium, Aspergillus and Candida. And the prevalent bacteria were gram-positive cocci. Airborne influenza A virus was not recovered in our study hospitals. The concentrations of total culturable bacteria and carbon dioxide (CO2) of the study hospitals were higher than the levels recommended by the Taiwan Environmental Health Administration. Indoor environmental quality of these hospitals need further improvement. High concentrations of total bacteria and CO2 might result from crowdedness and insufficient ventilation. Some departments had a higher level of ozone, probably resulting from high frequency of using copiers and printers. According to statistical analyses, exposure to droplets was associated with the respiratory illnesses of participants. Allergic diseases had significant associations with the number of patients cared per day and remodeling of working environment. Building related symptoms (BRS) were associated with too much or too little air movement, exposure to patient vomit, high temperature, and water-damage in working area. In order to improve health and productivity of their workers, hospitals should provide appropriate ventilation and take measures to control indoor pollutant levels.