Ethical considerations surrounding clinical research have been a topic of intense debate and discussion for many years, however, issues specific to the surgeon-scientist are rarely discussed. This article summarizes ethical issues pertinent to the surgeon-scientist including conflicts of interest, use of human biospecimens, data integrity, manuscript authorship, and mentorship for trainees. The methods include a review of the current and past literature on each of these topics with a brief overview of how it relates to the surgeon-scientist. Case examples are provided throughout to provide further discussion points related to the topic. The purpose of this review is to promote awareness of the ethical challenges that the surgeon-scientist faces when engaging in basic science research in order to spark discussion and encourage integrity and ethical behavior.