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8 year oldBuzzFeed CEO Jonah Peretti informed staff members by email on Monday.
The ads were due to run in the coming months and had been booked before Mr Trump became the presumptive nominee.
Mr Peretti told employees the move would have "no influence" on coverage of the campaign.
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Mr Peretti wrote: "We certainly don't like to turn away revenue (...) However, in some cases we must make business exceptions: we don't run cigarette ads because they are hazardous to our health, and we won't accept Trump ads for the exact same reason."
The website Politico reported that the deal had been worth $1.3m (£900,000).
Mr Peretti's email to staff continued as follows: "The Trump campaign is directly opposed to the freedoms of our employees in the United States and around the world and in some cases, such as his proposed ban on international travel for Muslims, would make it impossible for our employees to do their jobs."
Mr Trump defeated 16 other candidates for the Republican nomination for president. As he built up an unassailable lead in the primaries they d-ropped out one by one and last month, he secured the backing of enough delegates to win him the nomination.
Republicans will finalise their nomination at a convention in July.
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