Ethical challenges in genomic epidemiology are the direct result of novel tools used to confront scientific challenges in the field. An orders-of-magnitude increase in scale of genetic data collection has created the need for establishing diffuse international partnerships, sometimes across developed- and developing-world countries, with ramifications for assigning research ownership, distributing intellectual property rights, and encouraging capacity-building. Meanwhile, the fact that genomic epidemiological research is so far upstream in the pipeline of therapy development has implications for the privacy rights of research participants and for a rigorous definition of valid informed consent, particularly in resource-poor settings. From these scientific underpinnings, we distill out two main categories of ethical issues: (1) How should researchers ensure that the subjects of research are appropriately protected? and (2) What is the structure of an equitable and fair system for distributing the financial and scientific rewards of research? We attempt to delineate the contours of specific problems in each category and propose steps toward solutions with reference to a particular project, known as gMap.net, that focuses on genomic epidemiological studies of malaria.