Addressing increasing concerns about public health equity in the context of violent conflict and the consequent forced displacement of populations is complex. Important operational questions now faced by humanitarian agencies can to some extent be clarified by reference to relevant ethical theory. Priorities of service delivery, the allocation choices and the processes by which they are arrived at are now coming under renewed scrutiny in the light of the estimated two million refugees who fled from Iraq since 2003. Operational questions that need to be addressed include health as a relative priority, allocations between and within different populations, and transition and exit strategies. Public health equity issues faced by the humanitarian community can be framed as issues of resource allocation and issues of decision-making. The ethical approach to resource allocation in health requires taking adequate steps to reduce suffering and promote wellbeing, with the upper bound being to avoid harming those at the lower end of the welfare continuum. Deliberations in the realm of international justice have not provided a legal or implementation platform for reducing health disparities across the world, although norms and expectations, including within the humanitarian community, may be moving in that direction.Despite the limitations of applying ethical theory in the fluid, complex and highly political environment of refugee settings, this article explores how this theory could be used in these contexts, provides some practical examples, and encourages professionals in the field to consider these ethical principles when making decisions.