Background: There are limited empirical data on factors that influence ethical practices in research settings. To broaden our understanding of ethical practices in research in the U.S. Department of Veterans Affairs (VA) and to understand researcher- and organizational-level factors associated with positive perceptions of practices, we assessed researchers’ perceptions of practices in research ethics. Methods: We analyzed data from 10,661 respondents to the 2010 IntegratedEthics™ Staff Survey (IESS) at VA who self-identified as research staff and who worked at facilities with Federalwide Assurance for the Protection of Human Subjects. We used descriptive statistics to evaluate these respondents’ perceptions of ethical practices in research and multivariate logistic regression analyses to evaluate associations between researcher- and organization-level characteristics and positive perceptions of ethical practices. Results:The results suggest that the majority of researcher respondents have positive perceptions of ethical practices in research at VA; for example, 85% almost never feel pressured to compromise ethical standards. Physicians and staff with managerial responsibilities tend to have more favorable impressions of ethical practices in research. The results also indicate areas for improvement. For example, 14–16% of respondents report that there are research staff members who regularly engage in behaviors that may inappropriately affect their research. Furthermore, results suggest that approximately 14% of VA research staff are not completely comfortable raising ethical concerns or reporting ethical violations related to research. Conclusions: Results from this study identify areas for quality improvement that can serve as a complement to the required education and training in research ethics, policy guidance, and rigorous institutional review board oversight and monitoring.