Current DHHS regulations require that policies and procedures developed by institutions to handle allegations of scientific misconduct include provisions for “undertaking diligent efforts to protect the positions and reputations of those persons who, in good faith, make allegations.” Analogously, institutions receiving PHS funds are required to protect the confidentiality of those accused of such misconduct or, failing that, to restore their reputations if the allegations are not confirmed. Based on two surveys, one of whistleblowers and one of individuals accused but (...) exonerated of scientific misconduct, this paper examines how well the system works to protect both sets of participants in cases of alleged misconduct. Contrary to popular impressions created by notorious cases, substantial minorities of both whistleblowers and exonerated scientists experience no adverse outcomes at the time the allegations are made and pursued. During this period, however, whistleblowers report more negative outcomes and more severe negative outcomes than their accused but exonerated counterparts. In the longer run, majorities of both groups report little impact on different aspects of their careers or professional activities, though those who report any impacts generally report negative ones. The accused but exonerated, however, appear to fare worse than whistleblowers in impacts on several aspects of their personal lives; their mental health, physical health, self-esteem, and self-identity. (shrink)