We explore the experience of Navajo communities living under the shadow of nuclear age fallout who were subjects of five decades of research. In this historical analysis of public health (epidemiological) research conducted in the Navajo lands since the inception of uranium mining from the 1950s untill the end of the 20th century, we analyze the successes and failures in the research initiatives conducted on Navajo lands, the ethical breaches, and the harms and benefits that this research has brought about to the community. We discuss how scientific and moral uncertainty, lack of full stakeholder participation and community wide outreach and education can impact ethical decisions made in research.