Rehnquist, daughter of Chief Justice William Rehnquist and a former federal prosecutor, has been under investigation for several months. Three senators, led by Finance Committee Chairman Chuck Grassley, R-Iowa, last fall asked the General Accounting Office to look into accusations that she involuntarily transferred and forced resignations of more than a dozen senior fraud fighters in the agency.
Rehnquist was also being investigated for allegedly delaying an audit of Florida's pension fund until after the re-election of GOP Gov. Jeb Bush, the president's brother.
In her letter of resignation, Rehnquist said, "I feel it is important to spend more time with my teenage daughters and pursue other professional opportunities."
HHS Secretary Tommy Thompson praised Rehnquist's work in a statement.
"From the day she arrived at HHS, Janet articulated and carried out a clear and determined vision for fighting fraud and abuse," the secretary said. "Her first year on the job was a testament to her management and leadership, as she saved taxpayers $21 billion through enforcement activities -- a record year for her office."