The Center for Indoor Air Research (CIAR) was created by three United States tobacco companies in 1988. Its stated mission is to fund high-quality, objective research related to indoor air, including studies of environmental tobacco smoke (ETS). Because CIAR is financed by the tobacco industry and funds research related to tobacco, it fosters an inherent conflict of interest. We consider whether this conflict of interest has affected the content, quality, or use of research funded by CIAR. We hypothesize that the tobacco industry might be using CIAR to develop scientific data to support its position that ETS is not harmful to health. CIAR funds two types of projects: “Peer-reviewed” projects are awarded after peer review by a group of scientists, whereas “special-reviewed” projects are awarded directly by tobacco industry executives. CIAR’s special-reviewed projects are more likely than its peer-reviewed projects to be related to ETS, to support the tobacco industry position, and to be used by the industry to argue that smoking should not be regulated in public places. Our findings suggest that the tobacco industry is funding special-reviewed projects through CIAR to develop scientific data that it can use in legislative and legal settings. The industry may be financing peer-reviewed projects through CIAR to enhance its credibility, to provide good publicity, and to divert attention from ETS as an indoor air pollutant. CIAR’s stated mission of funding high-quality, objective research has been compromised by conflict of interest, and at least some of CIAR’s projects are being used to promote the tobacco industry’s agenda.