The increasing use and practice of complementary and alternative medicine (CAM) all over the world raises important ethical issues for health care providers, researchers and policy-makers. This article addresses the equity issues arising in the context of an evaluation of five complementary therapies provided by general practitioners: homeopathy, anthroposophic medicine, traditional Chinese medicine, neural therapy and phytotherapy. The evaluation was commissioned by the Swiss government in order to provide scientific data to make a policy decision about including these disciplines in basic insurance coverage, if provided by physicians. Both the research process and the related health policy raise a number of equity issues that are explored and further discussed on the basis of Daniels' and Sabin's criteria for fair decision-making as defined in their 'accountability for reasonableness' approach. Combining the lessons learnt from the case study with current approaches to fairness in decision-making and priority-setting, propositions are made in order to increase awareness for transparency and fairness in CAM-related evaluations and policy.