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Moral distress occurs when professionals are constrained from taking what they believe to be ethically appropriate actions or are forced to take actions they believe are ethically inappropriate, challenging their professional identities and representing systems‐level issues within organizations. Moral distress has been recognized in a variety of health care‐related fields; however, the phenomenon is still comparatively unexplored among clinical research professionals (CRPs). In this qualitative study, we interviewed ten CRPs to unearth root causes of moral distress in this ethically unique profession. Four themes emerged from the data as contributors to moral distress: commodification of research; concern for research participants; compromised science; and structures of hierarchy. The experience of racism as a source of moral distress is also explored. The findings of this study indicate that the existence of moral distress in clinical research is troubling not only for the welfare of CRPs but also for the greater clinical research enterprise.