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"We were able to win the game, but the referee scored a goal for Arsenal and that was earth-shattering," the 22-year-old explained.
"It's not acceptable. Referee Poll has cheated us. He clearly showed, he will give a whistle."
A statement from the FA read: "The FA can confirm that it is pursuing inquiries into media comments attributed to Chelsea goalkeeper Petr Cech about referee Graham Poll following his team's match at Arsenal on Sunday December 12."
"It came as a disappointment when phone-ins and the messages I received indicated that Henry's second goal was dominating so much of the post-game discussion," wrote Poll in his column in the Daily Telegraph.
"My initial thought was: controversy, what controversy?
"I received numerous requests to explain the situation but I did not speak to television, radio or the written press after the game, despite being 'quoted'.