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BACKGROUND: To provide prospective comparative data describing the profiles of two patient populations attending conventional or complementary medicine institutions. PATIENTS AND METHODS: A registration study was set up in an oncology ward at the Institute for Medical Oncology (IMO) of the University Hospital in Bern, and at the Lukas Clinic (LC) for Anthroposophical Cancer Treatment in Arlesheim, Switzerland. The same eligibility criteria were applied to enrol into the study all newly referred or newly diagnosed patients with advanced cancer over a 2-year period. Their socio- demographic and clinical characteristics at presentation have been compared between the two institutions. RESULTS: Patients at LC are primarily females, of higher educational level, and living in an urban environment. Patients at LC are also more frequently of poorer performance status but present with less comorbidity and a longer interval between diagnosis of metastatic disease and accrual into the study. CONCLUSION: This study suggests that the respective merits of these two schools of medicine can be assessed successfully only through a concrete research partnership based on rigorously controlled clinical trials.