As norms of comparative effectiveness research are sought within the biomedical and health care communities, and the science of conducting and interpreting this research develops, the Food and Drug Administration (FDA) must balance diverse interests. The agency’s overarching interest is the development of high-quality comparative effectiveness information that contributes to improved patient care. To further this interest, the FDA can provide expertise in trial design and postmarketing surveillance. The FDA can also ensure that manufacturers of medical products use comparative effectiveness information in product promotion in a manner consistent with regulatory requirements. In this article we observe that these requirements would preclude the manufacturer’s use in a promotional context of comparative effectiveness findings derived from an observational study. The FDA recognizes, however, that there are ongoing efforts to address the methodological problems inherent in observational approaches and to foster consensus on enhanced methods. The FDA must work to navigate challenges that relate to both the science of comparative effectiveness research and the agency’s statutory responsibilities to the public health.