Public participation is increasingly an aspect of policy development in many areas, and the governance of biomedical research is no exception. There are good reasons for this: biomedical research relies on public funding; it relies on biological samples and information from large numbers of patients and healthy individuals; and the outcomes of biomedical research are dramatically and irrevocably changing our society. There is thus arguably a democratic imperative for including public values in strategic decisions about the governance of biomedical research. (...) However, it is not immediately clear how this might best be achieved. While different approaches have been proposed and trialled, we focus here on the use of public deliberation as a mechanism to develop input for policy on biomedical research. We begin by explaining the rationale for conducting public deliberation in biomedical research. We focus, in particular, on the ELS (ethical, legal, social) aspects of human tissue biobanking. The last few years have seen the development of methods for conducting public deliberation on these issues in several jurisdictions, for the purpose of incorporating lay public voices in biobanking policy. We explain the theoretical foundation underlying the notion of deliberation, and outline the main lessons and capacities that have been developed in the area of conducting public deliberation on biobanks. We next provide an analysis of the theoretical and practical challenges that we feel still need to be addressed for the use of public deliberation to guide ethical norms and governance of biomedical research. We examine the issues of: (i) linking the outcomes of deliberation to tangible action; (ii) the mandate under which a deliberation is conducted; (iii) the relative weight that should be accorded to a public deliberative forum vs other relevant voices; (iv) evaluating the quality of deliberation; and (5) the problem of scalability of minipublics. (shrink)