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Implantable medical devices (IMD) are frequently used in interventional medicine. There are a host of complex methodological issues to consider in conducting device studies. A general conceptual framework for evidence evaluation is needed to help investigators conduct comparative studies in this setting. It is known that clinical trials of implants require study design planning and creative execution that are quite different from those in pharmaceutical setting. Important study design issues such as randomization, masking and allocation concealment require unique approaches for each device. In addition, device comparative studies must cope with sources of variability different from pharmaceutical studies. These include operator learning curve effects, hospital-operator-patient interactions, and issues related to device technical characteristics. Observational studies of IMDs are particularly challenging. Selection of comparison groups, adjusting for confounding and addressing learning curve issues needs careful planning. We propose a general framework for IMD evaluation and provide an outline of the methodological issues that require further discussion. We hope this article will inspire and help to inform those interested in advancing comparative safety and effectiveness of IMDs and to plan and pursue future methodological work in this area.