This review outlines recent advances in the investigation of the chemical properties, molecular interactions and health effects of hazardous compounds in atmospheric aerosols, in particular reactive oxygen species (ROS), soot, polycyclic aromatic compounds (PACs) and allergenic proteins. Epidemiological studies show correlations between air particulate matter and adverse health effects of air pollution including allergy, asthma, cardiovascular and respiratory diseases, but the causative relations and mechanisms of interaction on the molecular level are still unclear. ROS generated by photochemical and heterogeneous reactions in the atmosphere seem to play a key role in aerosol health effects and provide a direct link between atmospheric and physiological multiphase processes. Soot and PACs can trigger formation of ROS in vivo, leading to inflammation and cellular damage. PACs as well as allergenic proteins are efficiently oxygenated and nitrated upon exposure to ozone and nitrogen dioxide, which leads to an enhancement of their toxicity and allergenicity.