Anti-Islamic ads will begin appearing on 100 city buses and two subway entrances next week.
The six ads include an image of American journalist James Foley just before he was beheaded standing next to his masked executioner.
The ads are paid for by the American Freedom Defense Initiative run by anti-Islam blogger Pamela Geller. She says the campaign tells truths about Islam and Jihad that the U.S. government and mainstream media ignore.
All the ads feature a disclaimer that says the viewpoints are not endorsed by the MTA.
The agency is required under a federal court ruling to run controversial ads.
"We review every viewpoint ad under the standards, but a series of court rulings have made clear that our hands are largely tied," MTA spokesman Kevin Ortiz said.
The American Freedom Defense Initiative has posted ads in New York's transit system in the past that called enemies of Israel "savages."
