It is increasingly clear that a wide range of stakeholders should be included in the problem formulation phase of research aimed at solving environmental problems; indeed the inclusion of stakeholders at this stage has been formalized as an integral part of ecological risk assessment. In this paper, we advocate the additional inclusion of stakeholders in the refinement of research methods and protocols and in the execution of the research, rather than just at the final communication and reporting phase. We use a large study of potential radionuclide levels in marine biota around Amchitka Island as a case study. Amchitka Island, in the Aleutian Island Chain of Alaska, was the site of three underground nuclear tests (1965-1971). The overall objective of the biological component of the study was to collect a range of marine biota for radionuclide analysis that could provide data for assessing current food safety and provide a baseline for developing a plan to monitor human and ecosystem health in perpetuity. Stakeholders, including regulators (State of Alaska), resource trustees (US Fish and Wildlife Service, State of Alaska), representatives of the Aleut and Pribilof Island communities, the Department of Energy (DOE), and others, were essential for plan development. While these stakeholders were included in the initial problem formulation and approved science plan, we also included them in the refinement of protocols, selection of bioindicators, selection of a reference site, choice of methods of collection, and in the execution of the study itself. Meetings with stakeholders resulted in adding (or deleting) bioindicator species and tissues, prioritizing target species, refining sampling methods, and recruiting collection personnel. Some species were added because they were important subsistence foods for the Aleuts, and others were added because they were ecological equivalents to replace species deleted because of low population numbers. Two major refinements that changed the research thrust were (1) the inclusion of Aleut hunters and fishers on the biological expedition itself to ensure that subsistence foods and methods were represented, and (2) the addition of a fisheries biologist on a NOAA research trawler to allow sampling of commercial fishes. Although the original research design called for the collection of biota by Aleut subsistence fishermen, and by a commercial fishing boat, the research was modified with continued stakeholder input to actually include Aleuts and a fisheries biologist on the expeditions to ensure their representation. The inclusion of stakeholders during the development of protocols and the research itself improved the overall quality of the investigation, while making it more relevant to the interested and affected parties. Final responsibility for the design and execution of the research and radionuclide analysis rested with the researchers, but the process of stakeholder inclusion made the research more valuable as a source of credible information and for public policy decisions.