Complex global public health challenges such as the rapidly widening health inequalities, and unprecedented emergencies such as the pandemic of human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) demand a reappraisal of existing priorities in health policies, expenditure and research. Research can assist in mounting an effective response, but will require increased emphasis on health determinants at both the national and global levels, as well as health systems research and broad-based and effective public health initiatives. Civil society organizations (CSOs) are already at the forefront of such research. We suggest that there are at least three ways in which the participation of CSOs in research can be increased: namely, influencing commissioning and priority-setting; becoming involved in the review process and in conducting research; and through formal partnerships between communities and universities that link CSOs with academic researchers.