During the Clinton Administration, Rosenstein served as Counsel to Deputy Attorney General Philip B. Heymann (1993–1994) and Special Assistant to Criminal Division Assistant Attorney General Jo Ann Harris (1994–1995). Rosenstein then worked in the United States Office of the Independent Counsel under Ken Starr on the Whitewater investigation into President Bill Clinton. As an Associate Independent Counsel from 1995 to 1997, he was co-counsel in the trial of three defendants who were convicted of fraud, and he supervised the investigation that found no basis for criminal prosecution of White House officials who had obtained FBI background reports.