A method and apparatus is described for neutralizing airborne pathogens in ventilated air, and in heating or air conditioning systems. The pathogen neutralization system is effective against a wide spectrum of pathogens, it incorporates commercially available components, and it can be readily integrated into commercial HVAC systems where it neutralizes airborne pathogens in large volumes of ventilated air in real time without any chemical reagents. Typically, the system has a flow-through reaction chamber that contains a UV light source that emits short intense flashes of broad-spectrum UV light, a source of water vapor or spray, and an ozone generator. The system generates highly reactive ozone intermediates by irradiating ozone gas with UV light in the presence of water droplets or water vapor. The pathogens that can be neutralized by this system include bacteria, viruses, spores, fungi and parasites.