The American Freedom Defense Initiative purchased space next to 228 clocks in 39 stations for ads with an image of the burning World Trade Center 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 same group paid for ads to be displayed in 10 stations in September. Those ads implied enemies of Israel are "savages."
The MTA also sold space last year to competing advertisements that urged tolerance.