This paper describes and reflects upon a pilot study with user involvement. Patients chose between acupuncture and homoeopathy and were then randomised to this preference or to the control group of normal GP care. A total of 60 people with dyspepsia (≥ 2 weeks) presenting in one UK general practice were recruited in consultations and by letter to those on repeat prescriptions. There were few exclusion criteria. The homoeopath and the acupuncturist treated the patient individually according to their normal practice for up to 6 months. After the trial there was a focus group for participants. Outcome measures used SF-36 health survey, Measure Yourself Medical Outcome Profile (MYMOP), and General Well-being Index (GWBI). Counts of prescriptions, consultations and referrals from practice computer records. No trend or significant difference between the groups for clinical outcome or National Health Service costs were observed. Major costs for the 6 months [mean (SD) cost per patient] were: GP consultations, £8 (18); prescriptions, £64 (73); acupuncture, £175 (52); and homoeopathy, £105 (33). Participants gave insights and suggestions that will inform the full trial design.