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Franken, 66, a former comedian who had been seen as a rising star in the Democratic Party, said on the Senate floor he would be leaving in a few weeks.
"I know in my heart that nothing I've done as a senator - nothing - has brought dishonor on this institution," Franken said. "Nevertheless, today I am announcing that in the coming weeks, I will be resigning as a member of the United States Senate."
Franken is one of several prominent American men in politics, media and entertainment to be accused in recent months of sexual harassment and misconduct.
"Some of the allegations against me are simply not true. Others I remember very differently," Franken said.
The departure of the Minnesota Democrat presents an opening for Republicans to recapture a seat they lost when Franken won election in 2008, and to build on their slim 52-48 Senate majority.
The election to succeed him, however, will not be held until November 2018. In the interim, Minnesota's Democratic governor, Mark Dayton, will appoint someone to take his place, ensuring Democrats hold the seat for now.
"I have not yet decided on my appointment to fill this upcoming vacancy. I expect to make and announce my decision in the next couple of days," Dayton said in a statement.
Allegations that Franken had groped and tried to kiss women without their consent began to surface three weeks ago.
After the initial accusations, Franken said he was embarrassed and ashamed by his behavior but would not resign. Rather, he said, he would cooperate with a Senate ethics probe and work to regain the trust of the people of Minnesota.
However on Wednesday, calls for him to resign came from the majority of his Democratic colleagues in the Senate, including Democratic leader Chuck Schumer and almost all of the Democratic women in the chamber. That pressure came as a new allegation hit the news.
Politico reported that a congressional aide said Franken had tried to forcibly kiss her in 2006, before he was elected to the Senate. Franken denied the allegations, Politico reported.
Reuters has not independently verified the accusations against him.
'IRONY' IN DEPARTURE
Striking a somewhat defiant tone, Franken sought to contrast himself with two Republicans - President Donald Trump and Senate candidate Roy Moore.
"I, of all people, am aware that there is some irony in the fact that I am leaving while a man who has bragged on tape about his history of sexual assault sits in the Oval Office and a man who has repeatedly preyed on young girls campaigns for the Senate, with the full support of his party," he said.
In a 2005 videotape that surfaced last year as he was running for the White House, Trump was heard bragging about kissing and touching women. Trump apologized for the remarks, but called them private "locker-room talk" and said he had not done the things he talked about. Trump also denied allegations at that time by at least 12 women of sexual advances and groping in the past.
Reuters has not independently verified the accusations.
Moore, who is running for the Senate in Alabama, has been accused by several women of sexual assault or misconduct when they were teenagers and Moore was in his early 30s. Moore, 70, has denied the accusations, which Reuters has not independently verified.
Moore has been backed by Trump but Senate Republicans have been cooler toward his candidacy ahead of a special election on Tuesday.
In pressing Franken to step aside, Democrats have tried to capture the moral high ground and draw a distinction between their party and Republicans.
Democrat John Conyers, the longest serving member of the US House of Representatives, stepped down on Tuesday after multiple accusations of sexual misconduct, the first member of Congress to leave his seat during the wave of high-profile harassment allegations. Conyers has denied the allegations against him.
Several of Franken's Democratic colleagues dabbed tears from their eyes while he spoke. His family watched from the balcony.
Afterward, his Democratic colleagues lined up to embrace him, including many of the women who had called for his resignation.
The election to fill Franken's seat next year could be close.
When he ran in 2008, the race was decided after an extensive recount, with Minnesota's Supreme Court weighing in. In the 2016 presidential election, Democrat Hillary Clinton, won the state by less than two points.
Before he switched to politics, Franken rose to national prominence as a cast member on the long-running television program "Saturday Night Live."