Investigators at the FBI's New York office, who unsuccessfully argued for months that they should be allowed to open a full-blown investigation of the foundation, could find a more friendly audience in a Donald Trump administration Justice Department.
The President-elect railed during the closing weeks of the campaign against the relationship between foundation donors and Hillary Clinton's work in government as "corrupt."
He promised there would more investigations of the Clintons if he were elected.
Soon, top officials he appoints at the Justice Department will have the power make that happen.
And the FBI investigators may have more ammunition to make their case with stolen emails from Clinton aides released in recent weeks by WikiLeaks.
The emails showed internal fights over the foundation between Chelsea Clinton and a top aide to her father, Doug Band, who helped run the foundation. Chelsea Clinton, according to the emails, was concerned about possible conflicts of interest and problems related to Bill Clinton's paid speech-making business, dubbed "Bill Clinton Inc." The dispute prompted the foundation to conduct an internal audit of its activities. Band hit back at Chelsea Clinton, according to the emails, suggesting she used the foundation to pay for her wedding.
Rudy Giuliani, considered a contender for attorney general or other top cabinet post, according to people familiar with Trump transition planning, said Thursday that the new president will have to make a decision on what to do about his promises to hire a special prosecutor to investigate matters related to Clinton.
"It's been a tradition in our politics to put things behind us," Giuliani said on CNN's "New Day." "On the other hand, you have to look at how bad was it? Because suppose somebody comes along a year from now and is alleged to have stolen $50,000 from a charity -- and (Clinton) was never investigated for hundreds of millions."
Messages left with the Clinton Foundation seeking comment were not returned.
Career prosecutors at the Justice Department's criminal division and the public integrity section, as well as lawyers at the FBI, reviewed the requests earlier this year from FBI investigators to launch a full probe of the Clinton Foundation, according to law enforcement officials briefed on the discussions. The agents were told that they didn't have enough evidence to use more overt investigative methods, including seeking subpoenas, to open a full probe, the officials said. They were also told they could continue to gather information and revisit their requests if they found more evidence.
The genesis of the FBI efforts date, in part, to allegations published in the 2015 book "Clinton Cash" by conservative writer Peter Schweizer.
Agents were unhappy at being told they didn't have enough evidence, and that fed some of the tensions over Clinton-related matters inside the FBI in recent months between the New York field office and FBI headquarters, law enforcement officials say.
Trump repeatedly referred to the WikiLeaks emails -- in particular the issues raised by Band -- as proof that investigators should take a deeper look.
"Mr. Band called the arrangement unorthodox. The rest of us call it outright corrupt," Trump told an October campaign rally. "In fact, the Clinton Foundation even hired a law firm to find out if their pay to play scheme would jeopardize their charitable status with the IRS."
Trying to use the stolen emails released by WikiLeaks to try to build probable cause for further investigation could present legal hurdles for the FBI and the Justice Department.
At least some of the emails are labeled as "attorney-client privileged," meaning they have the legal protection of confidential communications between lawyer and client.
And then there's the fact the US government has declared that the emails were stolen by Russian intelligence in a cyber-hack of the email account of Clinton campaign chairman John Podesta.
Earlier this year, prosecutors in Manhattan US Attorney Preet Bharara's office used revelations from the Panama Papers, stolen and leaked legal documents from a law firm in that country that helped the rich create offshore financial shelters, as cause to issue subpoenas to individuals and firms named in the documents. Other lawyers at Justice Department headquarters debated whether the stolen materials could be used predicates for an investigation.