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Bill Gates was being investigated over an affair with a colleague at Microsoft prior to his resignation.
A spokeswoman for the billionaire said the affair ended 'amicably' and was not the reason behind his resignation from the board.
The spokeswoman said: "There was an affair almost 20 years ago which ended amicably.
"Bill's decision to transition off the board was in no way related to this matter. In fact, he had expressed an interest in spending more time on his philanthropy starting several years earlier."
Microsoft said it was conducting a 'thorough investigation'.
A spokesperson said: "Microsoft received a concern in the latter half of 2019 that Bill Gates sought to initiate an intimate relationship with a company employee in the year 2000.
"A committee of the board reviewed the concern, aided by an outside law firm, to conduct a thorough investigation.
"Throughout the investigation, Microsoft provided extensive support to the employee who raised the concern."
When he left Microsoft's board last year, Mr Gates said he was stepping down to focus on philanthropy.
He said: "I have made the decision to step down from both of the public boards on which I serve - Microsoft and Berkshire Hathaway - to dedicate more time to philanthropic priorities including global health and development, education, and my increasing engagement in tackling climate change.
"The leadership at the Berkshire companies and Microsoft has never been stronger, so the time is right to take this step."
He continued: "With respect to Microsoft, stepping down from the board in no way means stepping away from the company. Microsoft will always be an important part of my life's work and I will continue to be engaged with Satya and the technical leadership to help shape the vision and achieve the company's ambitious goals.
"I feel more optimistic than ever about the progress the company is making and how it can continue to benefit the world.
"I will continue to be engaged with Satya and the technical leadership to help shape the vision and achieve the company's ambitious goals.
"I am looking forward to this next phase as an opportunity to maintain the friendships and partnerships that have meant the most to me, continue to contribute to two companies of which I am incredibly proud, and effectively prioritize my commitment to addressing some of the world's toughest challenges."
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