Introduction: Comparative effectiveness research (CER) seeks to inform clinical decisions between alternate treatment strategies using data that reflects real patient populations and real-world clinical scenarios for the purpose of improving patient outcomes. There are multiple clinical situations where the unique characteristics of observational investigations can inform medical decision-making within the CER paradigm. Accordingly, it is critical for clinicians to appreciate the strengths and limitations of observational research, particularly as they apply to CER. Methods: This review focuses on the role of observational research in CER. We discuss the concept of evidence hierarchies as they relate to observational research and CER, review the scope and nature of observational research, present the rationale for its inclusion in CER investigations, discuss potential sources of bias in observational investigations as well as strategies used to compensate for these biases, and discuss a framework to implement observational research in CER. Conclusions: The CER paradigm recognizes the limitations of hierarchical models of evidence and favors application of a strength-of-evidence model. In this model, observational research fills gaps in randomized clinical trial data and is particularly valuable to investigate effectiveness, harms, prognosis, and infrequent outcomes as well as in circumstances where randomization is not possible and in studies of many surgical populations. Observational investigations must be designed with careful consideration of potential sources of bias and must incorporate strategies to control such bias prospectively, and their results must be reported in a uniform and transparent fashion. When these conditions can be achieved, observational research represents a valuable and critical component of modern CER.
