Evidence based practice (EBP) is a system of applying the most current and valid high quality evidence to support clinical decision making in a healthcare setting. In the twenty five years since its inception, EBP has become the accepted benchmark for excellence in healthcare. Although the system emerged within the biomedical sciences, in the years since EBP has become normative across all healthcare modalities from dentistry, allied health to complementary and alternative medicine (CAM). Practicing evidence based medicine within any modality potentially offers the patient the best available care based on high quality evidence. Yet it is the nature of the evidence that provokes some questions about the suitability of EBP across all modalities of healthcare. The meta analysis of randomized controlled trial (RCT) stands at the pinnacle of the hierarchy of evidence in EBP. This forms a challenge to CAM due to the difficulty in reducing the elementals of a holistic naturopathic assessment of a patient into an answerable question to be tested within a RCT. On one level this makes EBP paradigmatically incompatible with CAM, yet on another level it presents the opportunity to redefine the parameters of what is considered high level evidence. EBP has become a tool, and at times a weapon wielded by governments and health insurance companies to direct healthcare funding and policy. The implications of the nature of accepted evidence are becoming far reaching. The pursuit of the best available healthcare for each individual is the focus of EBP. However, the injudicious use of this system to direct health policy is fraught with biomedical bias and dominance. This issue raises the challenge to CAM to present high level evidence according to the rules of evidence, or face the annihilation of centuries of empirical knowledge.