A recent study in JAMA has garnered a lot of attention, but in my opinion tells us little that we did not already know. The main value of the study is to quantify an area that had previously not been formally surveyed.
The target of this survey by a group at Mass. General (plus my good friend Susan Dorr Gould at University of Michigan) was chairs of selected departments in U.S. medical schools. Of the two-thirds who responded, 60 percent had some form of personal relationship with industry, and 2/3 of the departments had some form of relationships with industry. (I would have guessed, myself, that the numbers would be higher.) In general, the chairs were not worried about these relationships having any negative impact on their department (now where have we heard that before?)
Campbell EG, Weissman JS, Ehringhaus S, et al. Institutional academic-industry relationships. JAMA 298:1779-86, Oct. 17, 2007.