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"Lance Armstrong has chosen to voluntarily resign from the Board of Directors of the Livestrong Foundation to spare the organisation any negative effects as a result of controversy surrounding his cycling career," Livestrong chairman Jeff Garvey said in a statement.
"We are deeply grateful to Lance for creating a cause that has served millions of cancer survivors and their families."
Armstrong, a survivor of testicular cancer, had previously stepped down as Livestrong's chairman.
The 41-year-old had his seven Tour de France victories nullified and was banned from cycling for life last month after the International Cycling Union (UCI) ratified the United States Anti-Doping Agency's (USADA) sanctions against him.
USADA published a report that said the now-retired rider had been involved in the "most sophisticated, professionalized and successful doping programme that sport has ever seen."
Livestrong spokeswoman Katherine McLane told Reuters that Armstrong "remains the inspiration" for the charity and is its largest donor, having contributed $7 million.
She said Armstrong will remain involved with Livestrong, just not as a board member.
Garvey added: "Lance Armstrong was instrumental in changing the way the world views people affected by cancer.
"His devotion to serving survivors is unparalleled and for 15 years, he committed himself to that cause with all his heart on behalf of the Livestrong Foundation."
Armstrong has denied ever using performance-enhancing drugs and the move comes a day after he tweeted a photograph of himself relaxing with his seven Tour de France winner's jerseys.