Microsoft may have to re-name a science initiative it launched only last week after a major science body with the same title cried foul.
Mr Gates announced the initiative in Prague last week
Bill Gates unveiled the EuroScience partnership scheme at a meeting in Prague, Czech Republic, on Wednesday.
But the Euroscience open forum, with a membership of over 2,100 (including several Nobel Laureates), expressed astonishment at the initiative's name.
Microsoft is now in talks with the body to try to reach an understanding.
"Mr Gates does not approve of software piracy, so I am sure he does not intend to steal our name," said Euroscience president Jean Patrick Connerade after hearing of the name for Microsoft's scheme.
"Euroscience is a registered association of scientists who give up time voluntarily in support of European Science.
"We have members in 40 European countries and, with the help of sponsors, we organise Esof, a pan-European Forum on all the sciences, to which thousands of people come."
Microsoft said it regretted any confusion caused by the use of the name EuroScience to describe its partnership scheme.
"Upon learning of the concern we immediately engaged with the Euroscience association and are in the process of addressing this misunderstanding," a spokesperson for the software giant told the BBC News website.
"For us, the name is not as important as the programme intention and if changing our programme name is the best way to collaboratively foster innovation, we are willing to change the name."
As part of its initiative, Microsoft plans to invest in a network of centres tied to key research institutions in Europe.
It said the goal of its initiative was to "accelerate fundamental innovation in science and computing through collaborative research programmes... across Europe".
After learning of the scheme's name, Dr Connerade said it would be difficult for people to distinguish which one was commenting on a particular matter of interest to the European science community.
"If Mr Gates wants to help us by injecting millions of dollars into Euroscience, then that is wonderful.
"But I am surprised - as the elected President of Euroscience, I was not consulted before Mr Gates made his speech to the Government Leaders' Forum in Prague," said Dr Connerade.