Swiss Federer will be bidding for his fourth consecutive title at Flushing Meadows, while Belgian Henin is hoping to repeat her 2003 triumph.
Organisers kept in line with the world rankings, with Spain's Rafael Nadal seeded two, Novak Djokovic of Serbia at three and Russian Nikolay Davydenko fourth.
Three other former champions are seeded in the men's event with American Andy Roddick fifth, 2001 winner Lleyton Hewitt of Australia 16th and 2000 champion Marat Safin of Russia at 25.
Defending women's champion Maria Sharapova of Russia is seeded second behind Henin, with Serb Jelena Jankovic third and Russian Svetlana Kuznetsova, the 2004 winner, fourth.
Wimbledon champion Venus Williams is 12th while her sister Serena, who has not played since Wimbledon, is eighth.
