Comparative effectiveness research (CER) has received substantial attention as a potential approach for improving health outcomes while lowering costs of care, and for improving the relevance and quality of clinical and health services research. The Institute of Medicine defines CER as ‘the conduct and synthesis of systematic research comparing different interventions and strategies to prevent, diagnose, treat, and monitor health conditions. The purpose of this research is to inform patients, providers, and decision-makers, responding to their expressed needs, about which interventions are most effective for which patients under specific circumstances.’ Improving the methods and infrastructure for CER will require sustained attention to the following issues: (1) Meaningful involvement of patients, consumers, clinicians, payers, and policymakers in key phases of CER study design and implementation; (2) Development of methodological ‘best practices’ for the design of CER studies that reflect decision-maker needs and balance internal validity with relevance, feasibility and timeliness; and (3) Improvements in research infrastructure to enhance the validity and efficiency with which CER studies are implemented. The approach to addressing each of these issues should be informed by the understanding that the primary purpose of CER is to help health care decision makers make informed clinical and health policy decisions. Copyright © 2010 John Wiley & Sons, Ltd.