This paper examines threats to scientific integrity posed by possible conflicts of interests that can occur when commercial entities participate in publicly funded research partnerships. Particular attention is given to the activities of the International Life Sciences Institute (ILSI), which presents itself as a society of learned individuals and groups working in the public interest. In reality, ILSI's members largely consist of commercial companies and corporate conglomerates involved in the manufacture of foods, beverages, chemicals and pharmaceuticals. The main conclusion is that conflicts of interest arising from third-party involvement in research partnerships are a threat to scientific integrity. Urgent action is needed by the scientific community to find ways to safeguard against threats to scientific integrity due to undeclared involvement of commercial entities in seemingly independent research and scholarship.