Despite the conciliatory tone struck in President-elect Donald Trump’s victory speech early Wednesday morning, the man who could run his Justice Department left the door wide open to prosecuting Hillary Clinton.

Rudy Giuliani, a former federal prosecutor, New York City mayor and a name on Trump's short list for attorney general, said Wednesday on Fox News' “The O’Reilly Factor” that Clinton was a legitimate target to be investigated and disputed that any prosecution would be political “payback.”

“There’s one tradition in America, right? Election is over. We forget about it. There is another tradition in America which is ‘equal justice under the law,’” Giuliani said. “And it would depend on how bad the violations are.”

CLINTON AIDE SAYS FOUNDATION PAID FOR CHELSEA'S WEDDING

FBI Director James Comey said on Sunday that recent revelations in the investigation into Clinton’s private, homebrew server did not cause him to change his recommendation to the Department of Justice to not pursue charges against the former secretary of state.

However, multiple reports indicate some in the FBI are also investigating the Clinton Foundation -- which has been the subject of scrutiny for whether donors got favorable treatment from the Clinton State Department -- something Giuliani noted on “O’Reilly.” Giuliani also said during a Thursday morning appearance on “Fox & Friends” that there were “deep, disturbing issues” regarding Clinton’s conduct.

Trump, then the Republican presidential nominee, first raised the prospect of prosecuting his Democratic opponent during an Oct. 9 debate.

“If I win, I am going to instruct my attorney general to get a special prosecutor to look into your situation because there has never been so many lies, so much deception,” Trump told Clinton.

But in the wee hours of Wednesday morning, with the election clinched, Trump gave kudos to Clinton for running a tough campaign, leaving out of his remarks any mention of the various scandals that often peppered speeches at his previous rallies.

“I mean, she fought very hard,” Trump said to a crowd who, just hours earlier, had chanted “Lock her up!” when Clinton appeared on a TV screen. “Hillary has worked very long and very hard over a long period of time, and we owe her a major debt of gratitude for her service to our country. I mean that very sincerely.”

Also complicating a prospective prosecution is the possibility that President Obama, on his way out of the Oval Office, could preemptively pardon Clinton for any federal crimes she may have committed (state and civil offenses would be exempt from such a pardon). The act would be reminiscent of President Ford pardoning President Nixon “for all offenses against the United States” during Nixon’s term in office after Nixon had resigned in the aftermath of the Watergate scandal.

Doing so would be a double-edged sword for Obama.

“So, the president can offer the pardon but the pardon carries an implication of guilt; if she accepts the pardon, her acceptance carries a confession of guilt,” Chapman University Law Professor Ronald Rotunda told FoxNews.com in an email.

Rotunda, however, noted that a pardon of just Clinton would leave any co-conspirators – potentially including former President Bill Clinton and top aides and foundation officials – open to prosecution. And if Clinton hypothetically confessed her guilt in the U.S., Clinton Foundation trustees around the world would also be at risk, according to charity fraud expert Charles Ortel.

Then there’s the potential battle over whether such a wide-ranging, non-specific presidential pardon is even legal. Ford’s pardon of Nixon was not challenged in court; however, Trump or Giuliani, who has been named as a leading attorney general candidate in numerous reports, could seek to do so.

Should Obama pardon Clinton, however, it could also prove beneficial for Trump, sparing the new president from having to undertake a messy and divisive legal fight so early in his administration. But Giuliani said the legal system, not Obama, should make the ultimate call.

Said Giuliani: “I think President Obama should leave it to the system we all believe in to determine ‘is she innocent or is she guilty?’”

FoxNews.com’s Malia Zimmerman contributed to this report.