Patient preferences have recently been highlighted as a potential threat to the validity of randomised controlled trials (RCTs). Although there have been significant methodological and statistical developments in relation to these issues, comparatively little attention has been paid to the development of a conceptual model concerning preferences and their effects on decision-making. This article describes the development of such a model, which was undertaken in parallel with a systematic review of the empirical data concerning preference effects. The model describes the concept of preference in terms of theoretical concepts from the psychological and economics literature, and describes a preliminary model of the development and operation of preferences in the context of RCTs. The paper then examines the implications of the model for informed consent and recruitment procedures. Key issues for future research are also outlined.