Background Increase in global health research undertaken in resource poor settings in the last decade though a positive development has raised ethical concerns relating to potential for exploitation. Some of the suggested strategies to address these concerns include calls for providing universal standards of care, reasonable availability of proven interventions and more recently, promoting the overall social value of research especially in clinical research. Promoting the social value of research has been closely associated with providing fair benefits to various stakeholders (...) involved in research. The debate over what constitutes fair benefits; whether those that addresses micro level issues of justice or those focusing on the key determinants of health at the macro level has continued. This debate has however not benefited from empirical work on what stakeholders consider fair benefits. This study explores practical experiences of stakeholders involved in global health research in Kenya, over what benefits are fair within a developing world context. Methods and results We conducted in-depth interviews with key informants drawn from within the broader health research system in Kenya including researchers from the mainstream health research institutions, networks and universities, teaching hospitals, policy makers, institutional review boards, civil society organisations and community representative groups. The range of benefits articulated by stakeholders addresses both micro and macro level concerns for justice by for instance, seeking to engage with interests of those facilitating research, and the broader systemic issues that make resource poor settings vulnerable to exploitation. We interpret these views to suggest a need for global health research to engage with current crises that face people in these settings as well as the broader systemic issues that produce them. Conclusion Global health research should provide benefits that address both the micro and macro level issues of justice in order to forestall exploitation. Embracing the two is however challenging in terms of how the various competing interests/needs should be balanced ethically, especially in the absence of structures to guide the process. This challenge should point to the need for greater dialogue to facilitate value clarification among stakeholders. (shrink)