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Research using randomised controlled trials to test the efficacy of the medicines used in homeopathy have generally concluded that no specific effects can be detected. Yet, homeopathy is a popular form of alternative medicine. RCTs are the most effective designs for testing a single hypothesis but inappropriate as the model to evaluate the effectiveness of homeopathy as a complex therapeutic intervention. Many RCT designs, though of high internal validity according to reductionist scientific paradigm, have misrepresented the holistic essence of homeopathy, so have low external validity.The non-reductionist paradigm of whole systems, or complex thinking, enables research into the synergism of various components of homeopathic treatment, because it acknowledges that the combined effects of parts of a system produce emergent properties not existent in the parts themselves. Health and disease are emergent properties of a human as a complex system (Bell, 2002).The study by Thompson and Weiss (2006) exemplifies WSR in action. It employs formal quantitative and qualitative means of data collection with which to triangulate results, which provides firmer evidence of the effectiveness of homeopathy than single case-studies alone. It has identified both specific and non-specific characteristics of the treatment. Many more pragmatic clinical trials of this nature will provide the evidence needed to balance the view that homeopathic effects are due to placebo action. Their innovative and ground-breaking study design heralds the beginning of a new phase in research away from RCT's in favour of WSR as the research model of choice in homeopathy.Key words: Homeopathy, research, whole systems research, WSR, randomised controlled trial, RCT, complex intervention, placebo, effectiveness