Background: To evaluate the clinical efficacy of treatment with integrated medicine (acupuncture and homeopathy in addition to conventional treatment) in improving measures of physical ability. Data from medical records with patient-reported information on background characteristics, diagnosis on admission (orthopaedic conditions and stroke) and movement performance indices. Methods: Comparative, observational, propensity-score matched clinical study. Participants: 383 adults admitted to the rehabilitation Centre in Manciano, stratified by stroke and orthopaedic condition. Interventions: acupuncture and homeopathy with physical rehabilitation vs. rehabilitation alone. Main outcome measures: Activities of daily living performance indices for patients with knee or hip replacements (Barthel index) and stroke patients (Barthel index and Trunk control test). Number of days of analgesic drug treatment for orthopedic patients. Results: The activities of daily living performance indices showed a significant improvement for both stroke patients (Fisher p-value: 0.008 and 0.046 for Barthel index and Trunk Control Test respectively) and orthopaedic patients (Fisher p-value: 0.032 for Barthel index) treated with integrated medicine. The treatment also reduced the duration of analgesic treatment by 2.8 days (Fisher p-value: 0.0015). Conclusion: Integrated medicine helps to improve rehabilitation performance in stroke and orthopaedic patients and considerably reduces the need for analgesic drugs.