Harrington carded a 6-under-par 66 on the Kingsbarns course to match his Thursday 66 at Carnoustie and sits at 12-under-par for the tournament. He closed strong, getting five birdies on his back nine, including two on the final two holes to top the leaderboard.
'It's half the battle to have 36 holes in and probably we have more than half the battle to go,' said Harrington. 'But that's nice, I'm there and it's always good to be in that position. It's better being where I am than trying to shoot two good scores on the weekend to get into contention.'
First-round leader Eduardo Romero followed up a 65 with a 4-under 68, also at Kingsbarns, and is in sole possession of second place. He had identical nines, each with five pars, three birdies and bogey, and is at 11-under after two days.
'I played very good yesterday and today and holed a few putts and got the ball on the fairway,' said Romero, the 48-year-old, who won the Scottish Open earlier in the year. 'I think Kingsbarn today was a little more windy than yesterday and a bit more difficult than Carnoustie so I'm pleased with that. St Andrews is my favorite golf course and I can't wait for tomorrow.'
Mikael Lundberg posted his second straight 67 while playing Carnoustie and used a five-hole stretch where he birdied four of five holes to get to 10-under and alone in third.
Dane Thomas Bjorn and Indias Jyoti Randhawa are together in fourth at minus-9.
Four players, including former two-time major winner Sandy Lyle, are just four off the pace with 8-under totals.
Retief Goosen and Vijay Singh, along with Ryder Cupper Philip Price, are tied at 7-under par and in a tie for 10th.
Ryder Cup hero Colin Montgomerie made a double eagle-2 on the par-5 third at Kingsbarns, which helped Monty get into a tie for 15th after Day 2. It was the first albatross of the season on the European Tour and turned out to be the difference in his round of 3-under 69.
'My first albatross was in Switzerland in 1990,' said Montgomerie, who is tied for 15th at five-under par. 'I shook Seve's (Ballesteros) hand on the first tee and then shook it again four minutes later when I holed my second shot.'
Full-field scores from the Dunhill Links Championships