OBJECTIVES: To develop a decision analysis based and computerised clinical guidance programme (CGP) that provides patient specific guidance on the decision whether or not to undergo a prophylactic oophorectomy to reduce the risk of subsequent ovarian cancer and to undertake a preliminary pilot and evaluation. SUBJECTS: Women who had already agreed to have a hysterectomy who otherwise had no ovarian pathology. SETTING: Oophorectomy decision consultation at the outpatient or pre-admission clinic. METHODS: A CGP was developed with advice from gynaecologists and patient groups, incorporating a set of Markov models within a decision analytical framework to evaluate the benefits of undergoing a prophylactic oophorectomy or not on the basis of quality adjusted life expectancy, life expectancy, and for varying durations of hormone replacement therapy. Sensitivity analysis and preliminary testing of the CGP were undertaken to compare its overall performance with established guidelines and practice. A small convenience sample of women invited to use the CGP were interviewed, the interviews were taped and transcribed, and a thematic analysis was undertaken. RESULTS: The run time of the programme was 20 minutes, depending on the use of opt outs to default values. The CGP functioned well in preliminary testing. Women were able to use the programme and expressed overall satisfaction with it. Some had reservations about the computerised formal and some were surprised at the specificity of the guidance given. CONCLUSIONS: A CGP can be developed for a complex healthcare decision. It can give evidence-based health guidance which can be adjusted to account for individual risk factors and reflects a patient's own values and preferences concerning health outcomes. Future decision aids and support systems need to be developed and evaluated in a way which takes account of the variation in patients' preferences for inclusion in the decision making process.