A retrospective audit was carried out on 58 patients with chronic health problems who were referred by 22 general practitioners (GPs) for acupuncture, aromatherapy, homeopathy, massage and osteopathy, or a combination. Costs of GP consultations, prescriptions, secondary care referrals, and diagnostic tests from records of 33 of these patients were compared pre (24 months), during (mean 4.3 months) and post (mean 5.7 months) complementary medicine (CM) treatment. Patient centred outcome data included the Measure Yourself Medical Outcome Profile (MYMOP) and content analysis of patient and practitioner comments. Costs of GP consultations/patient/month were significantly higher during (20.10 pounds, p<0.001) and post (17.53 pounds, p<0.01) CM treatment compared with pre-treatment costs (11.27 pounds). Total prescription costs were not significantly higher during and post-treatment than pre-treatment. Prescription costs for referred conditions were lower during (2.26 pounds) and higher post-treatment (3.75 pounds) compared with costs pre-treatment (3.24 pounds). Pre- and post-treatment MYMOP scores indicated significant improvements in health and well-being. Longer follow up, is required in order to demonstrate significant cost savings related to CM provision. Cost comparisons with conventional medicine should consider quantitative and qualitative data to capture the wider benefits experienced by patients.