What is a conflict of interest? Gilbert's Law Dictionary says that a conflict of interest (COI) arises when private interests clash with one's duty to serve the public interest. Prejudicial interest refers to having an interest in a topic that may affect one's ability to fairly and objectively consider the subject. Equipoise is a scientific concept by which a researcher believes in a hypothesis, yet no factual proof yet exists. Equipoise becomes conflict when medical professionals convince themselves they are right despite evidence to the contrary because of their own self-interests. When that happens, an ethical line in the sand is crossed. It can be hard to tell when that line gets crossed, no matter how rigorously a decision, affiliation, or financial arrangement is examined.

There are a panoply of new standards, rules, and guidelines relating to COI for medical research. The Physician Payment Sunshine provisions under the Patient Protection and Affordable Care Act mandate medical product and device companies to report any kind of transfer of value to physicians and post it in a public database. A half dozen states, with more likely to follow, have rules governing conduct for pharmaceutical and medical-device manufacturers that require reporting, prohibit, or impose restrictions on a wide array of physician–industry activities ranging from free meals to continuing medical education courses. At the federal level, rules under the National Institutes of Health (NIH) require medical researchers receiving federal grants to disclose any industry payments over $5000 and allow a university's NIH grants to be withdrawn for egregious violations or lack of oversight.

In the private sector, medical researchers are required by some medical publications to fill out standardized forms that enumerate payments from consulting work, honoraria, expert testimony, grants, commissioned manuscripts, intellectual property rights, royalties, stock holdings, and advisory boards. The American Medical Students Association ranks medical schools annually based on their COI polices, and the Pew Prescription Project and Yale University both have conducted recent surveys of patient attitudes regarding physician ties to pharmaceutical companies.