Abstract Background An international panel of experts was convened to examine the challenges faced in conducting economic analyses of Complementary, Alternative and Integrative Medicine (CAIM). Methods A one and a half-day panel of experts was convened in early 2011 to discuss what was needed to bring about robust economic analysis of CAIM. The goals of the expert panel were to review the current state of the science of economic evaluations in health, and to discuss the issues involved in applying these methods to CAIM, recognizing its unique characteristics. The panel proceedings were audiotaped and a thematic analysis was conducted independently by two researchers. The results were then discussed and differences resolved. This manuscript summarizes the discussions held by the panel members on each theme. Results The panel identified seven major themes regarding economic evaluation that are particularly salient to determining the economics of CAIM: standardization (in order to compare CAIM with conventional therapies, the same basic economic evaluation methods and framework must be used); identifying the question being asked, the audience targeted for the results and whose perspective is being used (e.g., the patient perspective is especially relevant to CAIM because of the high level of self-referral and out-of-pocket payment); the analytic methods to be used (e.g., the importance of treatment description and fidelity); the outcomes to be measured (e.g., it is important to consider a broad range of outcomes, particularly for CAIM therapies, which often treat the whole person rather than a specific symptom or disease); costs (e.g., again because of treating the whole person, the impact of CAIM on overall healthcare costs, rather than only disease-specific costs, should be measured); implementation (e.g., highlighting studies where CAIM allows cost savings may help offset its image as an “add on” cost); and generalizability (e.g., proper reporting can enable study results to be useful beyond the study sample). Conclusions The business case for CAIM depends on economic analysis and standard methods for conducting such economic evaluations exist. The challenge for CAIM lies in appropriately applying these methods. The deliberations of this panel provide a list of factors to be considered in meeting that challenge.