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BACKGROUND In South Korea, a few patients with low back pain (LBP) are currently being treated with a combination of traditional Korean medicine (KM) and Western medicine (WM). Although a recent research has reported results regarding patient satisfaction and exploratory effectiveness, evidence of comparative effectiveness still needs to be reviewed. The aim of this study is to evaluate the clinical and cost-effectiveness of KM and WM collaborative treatment (CT) compared with that of sole treatment (ST) for patients with LBP in Korea. METHOD/DESIGN This multisite, prospective observational comparative effectiveness research study is part of a nationwide pilot project for KM and WM collaboration launched by the Korean Ministry of Health and Welfare. The duration of the study is 8 weeks, and the target number of inclusion is 360 patients. Participants receive treatment according to their treatment plan, and a researcher conducts investigations thrice, every 4 weeks. In the final analysis, the merged data from the participants' questionnaire responses, hospital medical records, and administrative data, and Health Insurance Review and Assessment service data will be compared between the CT and ST groups. DISCUSSION This study will provide clinical and economic information about CT for LBP, which might be a milestone for establishing future polices about this collaboration in Korea. TRIAL REGISTRATION The study protocol has been registered with the Clinical Research Information Service (KCT0002827).