Even so, the Clinton Foundation's ranking on the list served as a black eye on the time, coming in the weeks just after Hillary Clinton announced she was stepping down from the charity's board to run for president. Increased scrutiny showed overlaps between Bill and Hillary Clinton's personal and political supporters and donors to the charity. In addition, The Washington Post revealed in February that the foundation had accepted millions of dollars in donations from foreign governments while Clinton was secretary of state, including one donation that came in violation of an ethics agreement with the Obama administration.

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In a note posted to its website, Charity Navigator indicated that tax information made available by the Clinton Foundation, including four years of returns amended by the organization last month, as well as a public memo submitted by the group, met Charity Navigator's requirements for removal.

Charity Navigator will continue its practice of offering the Clinton Foundation no formal rating, indicating that it has an "atypical business model" that cannot be "accurately captured" by the group's current rating methodology. However, the Clinton Foundation received an "A" earlier this year for financial performance from the American Institute of Philanthropy's Charity Watch, the nation's other leading watchdog organization for charities.

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The Clinton Foundation was formed by Bill Clinton before he left the White House, first to raise funds for his presidential library and then to serve as a vehicle for his post-presidential charitable ambitions. It has grown into a $2 billion empire that employs 2,000 people and works to improve health care, education and economic development all around the globe. Hillary Clinton joined the organization after she stepped down from the State Department in 2013. Former first daughter Chelsea Clinton has also taken on an increasingly larger role at the organization in recent years and now serves as its vice chairman.

The foundation's work had largely received bipartisan praise before the presidential campaign began. But this year, its operations have been the subject of significant Republican criticism, particularly from those who believe that donors to the organization might have sought special access to Clinton's State Department or might be hoping for special favor if Hillary Clinton is elected president. The Clintons and foundation officials have rejected those suggestions and have sought to demonstrate the charity's work has continued uninterrupted, even amid the campaign year scrutiny.

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The Chronicle of Philanthropy first reported the Clinton Foundation's removal from the list.