When, as a condition of the Master Settlement Agreement (MSA) in 1998, US tobacco companies disbanded the Council for Tobacco Research and the Center for Indoor Air Research, they lost a vital connection to scientists in academia and the private sector. The aim of this paper was to investigate two new research projects funded by US tobacco companies by analysis of internal tobacco industry documents now available at the University of California San Francisco (San Francisco, California, USA) Legacy tobacco documents library, other websites and the open scientific literature. Since the MSA, individual US tobacco companies have replaced their industry-wide collaborative granting organisations with new, individual research programmes. Philip Morris has funded a directed research project through the non-profit Life Sciences Research Office, and British American Tobacco and its US subsidiary Brown and Williamson have funded the non-profit Institute for Science and Health. Both of these organisations have downplayed or concealed their true level of involvement with the tobacco industry. Both organisations have key members with significant and long-standing financial relationships with the tobacco industry. Regulatory officials and policy makers need to be aware that the studies these groups publish may not be as independent as they seem.