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The new science of genomics endeavors to chart the genomes of individuals around the world, with the dual goals of understanding the role genetic factors play in human health and solving problems of disease and disability. From the perspective of indigenous peoples and developing countries, the promises and perils of genomic science appear against a backdrop of global health disparity and political vulnerability. These conditions pose a dilemma for many communities when attempting to decide about participating in genomic research or any other biomedical research. Genomic research offers the possibility of improved technologies for managing the acute and chronic diseases that plague their members. Yet, the history of particularly biomedical research among people in indigenous and developing nations offers salient examples of unethical practice, misuse of data, and failed promises. This dilemma creates risks for communities who decide either to participate or not to participate in genomic science research. Some argue that the history of poor scientific practice justifies refusal to join genomic research projects. Others argue that disease poses such great threats to the well-being of people in indigenous communities and developing nations that not participating in genomic research risks irrevocable harm. Thus, some communities particularly among indigenous peoples have declined to participate as subjects in genomic research. At the same time, some communities have begun developing new guidelines, procedures, and practices for engaging with the scientific community that offer opportunities to bridge the gap between genomic science and indigenous and/or developing communities. Four new approaches warrant special attention and further support: consulting with local communities; negotiating the complexities of consent; training members of local communities in science and health care; and training scientists to work with indigenous communities. Implicit is a new definition of “rigorous scientific research,” one that includes both community development and scientific progress as legitimate objectives of genomic research. Innovative translational research is needed to develop practical, mutually acceptable methods for crossing the divide between genomic researchers and indigenous communities. This may mean the difference between success and failure in genomic science, and in improving health for all peoples.