Purpose: To examine the effects that existing courses on the responsible conduct of research (RCR) have on ethical decision making by assessing the ethicality of decisions made in response to ethical problems and the underlying processes involved in ethical decision making. These processes included how an individual thinks through ethical problems (i.e., meta-cognitive reasoning strategies) and the emphasis placed on social dimensions of ethical problems (i.e., social-behavioral responses). Method: In 2005-2007, recruitment announcements were made, stating that a nationwide, online study was being conducted to examine the impact of RCR instruction on the ethical decision making of scientists. Recruitment yielded contacts with over 200 RCR faculty at 21 research universities and medical schools; 40 (20%) RCR instructors enrolled their courses in the current study. From those courses, 173 participants completed an ethical decision-making measure. Results: A mixed pattern of effects emerged. The ethicality of decisions did not improve as a result of RCR instruction and even decreased for decisions pertaining to business aspects of research, such as contract bidding. Course participants improved on some meta-cognitive reasoning strategies, such as awareness of the situation and consideration of personal motivations, but declined for seeking help and considering others' perspectives. Participants also increased their endorsement of detrimental social-behavioral responses, such as deception, retaliation, and avoidance of personal responsibility. Conclusions: These findings indicated that RCR instruction may not be as effective as intended and, in fact, may even be harmful. Harmful effects might result if instruction leads students to overstress avoidance of ethical problems, be overconfident in their ability to handle ethical problems, or overemphasize their ethical nature. Future research must examine these and other possible obstacles to effective RCR instruction.