The American Freedom Defense Initiative purchased space next to 228 clocks in 39 stations for the ads, which have an image of the twin towers burning and a quote attributed to the Quran saying: "Soon shall we cast terror into the hearts of the unbelievers."
The Metropolitan Transportation Authority said the ads went up Monday and will run for a month.
The group's earlier ads were displayed in 10 stations in September.
The agency has also sold space to groups that disagree with those messages.
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