Background Clinical research encompasses a wide variety of disciplines. Traditional Chinese medicine (TCM) and natural product research have made great contributions to preventing and treating illness. The number and content of original research reports evaluating TCM and natural products have not previously been described. Information in this area will identify areas of relative strength and weakness in terms of knowledge gaps with respect to clinical conditions and natural product remedies.Methods Original research reports (i.e. original articles, brief reports, and research letters) published in the Chinese Medical Journal (CMJ) from January 2000 to December 2009 evaluating TCM and other natural products were reviewed.The United Kingdom Clinical Research Collaboration (UK-CRC) Health Research Classification System was used to analyze the type of health research conducted. Further analysis on the major illnesses addressed and the major herbal components utilized was conducted.Results One hundred and seventeen original research reports involving TCM or other natural products were identified,comprising 3.82% of the CMJ output in the period covered by this study. Of the different materia medica described in these reports, 74.4% were derived exclusively from plant material, 10.3% from animals, 3.4% from fungi, 1.7% from minerals, and 10.3% were of mixed (plant / animal / fungal / mineral) composition. Twelve herbs were investigated exclusively or were constituents of 66/87 (75.9%) of the plant-based materia medica investigated. Panax ginseng was the most commonly investigated herb or constituent (14/87, 16.1%), followed by Astragalus membranaceus (9/87, 10.3%),Coptis chinensis/Berberis spp. (7/87, 8.0%) and Rheum spp. (7/87, 8.0%). Four UK-CRC health categories accounted for the majority of TCM and other natural product research (cancer, 20.9%; cardiovascular, 19.2%; oral/gastrointestinal,9.8%; and inflammatory/immune, 9.0%). The most common research activity was "development of treatments and therapeutic interventions", which was undertaken by 103/117 (88.0%) of the research investigations reported. Human clinical trials involving natural products accounted for only 5.31% of the reported studies.Conclusions This is a relatively early systematic description of published research from a single joumal related to TCM and other natural products. The majority of the research reports described preliminary findings and very few controlled clinical trials in human subjects were reported. Further applied studies will be required to demonstrate the clinical effectiveness, utility and cost-effectiveness of TCM and natural products in clinical practice. The UK-CRC health research classification system is a useful tool for evaluating published research output and could be applied to describe the output from other journals, national and provincial funding bodies, charities, and non-governmental organizations involved in supporting health-related research.