This paper brings understanding to the ethical dimensions of human health research conducted in the context of contaminated sites. Principle-based ethical analysis, complemented with virtuous traits of character, aid in bringing clarity to recommendations for actions following research. Epidemiology is the discipline for conducting health research not only because of its methodological foundations, but also because of its social justice focus. Because contaminated sites include communities that have been exposed to excessive concentrations of hazardous substances, extra care is needed when using epidemiology. For instance, vigilance over potential influence and engagement with affected communities are needed. Community engagement not only aids in understanding the contextual framework, but also demonstrates respect for both community and individual autonomy. Ethical analysis makes transparent the rationale for decisions against which researchers can be held accountable and provides a basis for evaluating observed outcomes as a function of the rationale provided for past actions.