Hospitals and other health care facilities are complex environments that require specialised ventilation for the comfort of patients, personnel and visitors and to control hazardous emissions. Among the most highly specialised environments in hospitals are operating theatres. Health care personnel who work in surgical suites are potentially exposed to a number of airborne hazards and an environment that relies on ventilation to achieve a high air quality. We have tried to compare such environments in two very different hospitals with different exposures to different risk factors. The hospitals were the University Hospital in Prague which is located in the centre of the city in historical buildings and Homolka Hospital. The latter is one of the newest mono-block hospitals in Prague, well equipped; smaller than the University Hospital but specialised (with Leksell Gamma Knife facilities for neurosurgery). We compared the concentrations of anaesthetic gases and room temperature during operations in theatres at the two hospitals with or without air-conditioning. The positive effect of ventilation systems was confirmed provided the systems were properly operated and well maintained. However, it is best to identify and control at source airborne pollutants since this is the most effective way of reducing or preventing of indoor air quality problems, followed by other measures including ventilation.