The substantial research activity, over which he presides, spans all aspects of air pollution research from toxicology through to science policy. The experimental research examines the toxicity of airborne particulate matter, diesel and biodiesel exhaust emissions, wood smoke and identifies of biomarkers of exposure. A new area of investigation is ambient microplastics, where work is focusing on their identification, detection and potential health effects. He has led studies on the urban airshed within London, including the impact of the introduction of London’s Congestion Charging Zone and the Ultra Low Emission Zone. During his leadership at King’s, the London Air Quality Network developed into a first class dissemination and education resource for London residents.

New areas of research interest include, 1) the impact of climate change air quality and hence health through increasing harmful ground-level ozone and increasing exposure to allergens like pollen an 2) indoor air quality. Children growing up in the UK today represent an 'indoor child generation', with most of their activities taking place within enclosed spaces, primarily homes and schools, with chemically diverse and often complex air quality environments. Even so, despite its importance in human exposure terms, links between indoor air quality in its widest sense and public health is a relatively under-researched area.

Professor Kelly has published over 450 peer-reviewed papers as well as many conference papers and books (as author or editor) on the toxicology and health effects of ozone, nitrogen dioxide and particulate pollution. He provides policy support to the World Health Organisation on air pollution issues and is a member of the Health Effects Institute (HEI) Review Committee. He is past Chairman of COMEAP, the UK’s Department of Health’s Expert Committee on the Medical Effects of Air Pollutants, past President of the European Society for Free Radical Research and past Chairman of the British Association for Lung Research.