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The Northern Irishman has struggled on his second-round outings of late, but he was near-perfect at the Royal Liverpool club to run away from the chasing pack.
The two-time Major champion bogeyed the first hole before recovering strongly with three birdies on the front nine, and a strong finish saw him close on 12-under par, four strokes clear of Dustin Johnson.
McIlroy picked up a shot at the par-three 15th, before making an impressive save from the sand at the next hole. A booming 390-yard drive set up a birdie at 17 and he finished with another at 18.
It was Johnson who recorded the round of the day, thriving in the best of the conditions to go seven-under-par and rocket up the leaderboard. He, like McIlroy, closed with successive birdies.
Americans and South Africans were the big movers as former Major winners Louis Oosthuizen and Charl Schwartzel moved into a pack at six-under which also includes Ryan Moore, Sergio Garcia, Rickie Fowler and Francesco Molinari.
Tiger Woods needed a birdie on the 18th to make the cut, but his five-over-par 77 means that he is likely out of contention heading into the weekend, unlike world number one Adam Scott and the in-form Justin Rose, who are three and two under respectively after 36 holes.