Complementary medicine has a different philosophy from conventional medicine, presenting challenges to research methodology. Rigorous evaluation of complementary medicine could provide much needed evidence of its effectiveness. Good design of randomised controlled trials will avoid invalid results and misrepresentation of the holistic essence of complementary medicine. Practitioners need to be recognised as a component in or contributor to complementary treatment. Both specific and non-specific outcome measures with long follow up are needed to adequately encompass the essence of complementary medicine