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Background  Economic evaluation focuses on Quality-Adjusted-Life-Years (QALYs) as the main valuation method. However, it is well known that factors beyond health related quality of life are important to patients and the public. Whilst discrete-choice-experiments (DCE) have been extensively used to value such factors, their incorporation within an economic evaluation framework is limited. This study is the first to incorporate patient preferences for factors beyond QALYs into an economic evaluation and compare results with the standard cost-per-QALY approach, using randomised-controlled-trial (RCT) participants.    Methods  Costings, clinical-effectiveness (appropriateness-of-treatment), QALYs and patient satisfaction data were collected at baseline and 12-month follow-up for a new pharmacy-service within a randomised-controlled-trial. Trial participants who replied to the follow-up survey and had not subsequently withdrawn from the study were mailed a DCE questionnaire at 24-months. WTP for the standard and new service was derived from the DCE. Results from QALYs and the DCE were compared.    Results  At 12 months, costs, clinical-effectiveness and QALYs did not differ between the  intervention  and  control ; however there was a significant increase in satisfaction in the  intervention . The DCE valued this increased satisfaction in the  intervention  (positive net-benefit). The longer the time patients experienced the new service the greater the reported net-benefit.    Conclusion  When incorporating a DCE into an economic evaluation a number of questions are raised:  what  factors should be valued,  whose  values (trial-groups vs. all–trial-population) and  when  should they be elicited (still-receiving-the-intervention or afterwards). Consideration should also be given to status  quo  bias.    Electronic supplementary material  The online version of this article (doi:10.1186/s13561-016-0108-4) contains supplementary material, which is available to authorized users.

What, who and when? Incorporating a discrete choice experiment into an economic evaluation