In addition to being influenced by the environment, the indoor air pollution in hospitals may be associated with specific compounds emitted from various products used, health care activities and building materials. This study has enabled assessment of the chemical and microbiological concentrations of indoor air in two French hospitals. Based on an integrated approach, the methodology defined aims to measure concentrations of a wide range of chemical compounds (>50 volatile and semi-volatile organic compounds), particle concentrations (PM and PM), microorganisms (fungi, bacteria and viruses) and ambient parameters (temperature, relative humidity, pressure and carbon dioxide). Chemical and microbiological air concentrations were measured during two campaigns (winter and summer) and across seven rooms (for spatial variability). The results have shown that indoor air contains a complex mixture of chemical, physical and microbiological compounds. Concentrations in the same order of magnitude were found in both hospitals. Compared to dwelling indoor air, our study shows low, at least equivalent, contamination for non-hospital specific parameters (aldehydes, limonene, phthalates, aromatic hydrocarbons), which is related to ventilation efficiency. Chemical compounds retrieved at the highest concentration and frequencies are due to healthcare activities, for example alcohol - most commonly ethanol - and hand rubbing (median concentration: ethanol 245.7 μg/m and isopropanol 13.6 μg/m); toluene and staining in parasitology (highest median concentration in Nancy laboratory: 2.1 μg/m)).