Private industry funds more than half of all medical research in the United States. While industry involvement in research has benefits, it can also create conflicts of interest. The most common policies adopted to address conflict of interest in medical research are focused primarily on the ways in which industry sponsorship may undermine a clinician’s judgment regarding patient care. Insufficient attention has been given to the ways in which industry sponsorship may undermine judgment relative to the goal of scientific integrity in research. The most common conflict of interest policies do not adequately address this problem. Disclosure policies alone will not remove or ameliorate all conflicts. Further, severing or monitoring ties between clinicians and industries will not adequately address the problem, since in many cases it is not the clinicians who are making the relevant research judgments. In order to address the problem of conflict of interest inindustry-sponsored research, fundamental changes in strategy and practice must be adopted which either remove the power to make research decisions from industry employees, or increase the review of those decisions by independent investigators.