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When conducting research with American Indian tribes, informed consent beyond conventional Institutional Review Board (IRB) review is needed because there may be potential for adverse consequences at a community or governmental level that are unrecognized by academic researchers. This paper reviews sovereignty, research ethics, and data-sharing considerations when doing community-based participatory health-related or natural resource-related research with American Indian nations and presents a model material and data-sharing agreement that meets tribal and university requirements. Only tribal nations themselves can identify potential adverse outcomes, and they can do this only if they understand the assumptions and methods of the proposed research. Tribes much be truly equal partners in study design, data collection, interpretation, and publication. Advances in protection of intellectual property rights are also applicable to IRB reviews, as are principles of sovereignty and indigenous rights, all of which affect data ownership and control. Academic researchers engaged in tribal projects should become familiar with all three areas: sovereignty, ethics and informed consent, and intellectual property rights (IPR). We recommend developing an agreement with tribal partners that reflects both health-related IRB and natural resource-related IPR considerations.