DUBAI, January 31, 2014 (AFP) - The Ulsterman struggled off the tees early on in his second round, but by the turn he had briefly eased three strokes clear of the field, only for his putting woes and a charge by rising US star Brooks Koepka to keep him in check.
McIlroy had a 70 to stand at 11-under 133, with Koepka, a year younger than McIlroy at 23, equalling the day's best round of 65 to get to 10 under.
"It was a round that could have been much better. Still, shooting a couple under par and finishing with a nice birdie the way I did. I'm leading the golf tournament. I've been in this position before and I've gone on to win," McIlroy said.
Three strokes off the pace on eight under came Damien McGrane (70) of Ireland, Englishman Danny Willett (65) and Julien Quesne of France (70).
Defending champion Stephen Gallacher of Scotland (71) and European number one Henrik Stenson of Sweden (67) were among those on seven under.
It was another disappointing day for Tiger Woods, who struggled with the putter all the way en route to a 73, which left him eight shots adrift of playing partner McIlroy and well down the field.
Looking to make it two wins and a second place in his last three tournaments, McIlroy had the luxury of taking the morning off watching to see whether anyone could overhaul him after his stunning nine-under 63 on Thursday.
Several challengers came and went, especially McGrane, Willett and Italian Ryder Cup star Edoardo Molinari.
But no-one was able to dislodge McIlroy from the lead.
For a brief moment it looked like he would do that all by himself as he started his second round with three wayward drives.
He dropped one at the first, but scrambled to save par at the second, and a superb bunker shot at the par-five third gave him a birdie as he got back to nine under.
Watched by wife-to-be, tennis player Caroline Wozniacki, McIlroy then birdied the fifth and the seventh to increase his lead at the top to three shots.
But just when it looked like he was about to clamp a serious stranglehold on a tournament which was his first triumph as a professional in 2009, McIlroy let it briefly slip - missing a two-footer for par at the 13th and erring off the tee at the 16th.
Koepka, who opted to play on the European Tour Challenger circuit after graduating from his US college in May, 2012, was flawless with seven bogeys in his 65.
"It reminds me a lot of American courses," the Floridian said. "It's weird, it's a course set up for a drawer and I fade the ball. So it's a little tougher for me, but I've been playing well so I can't complain."
Woods, playing in his second tournament of the year after missing the final cut at Torrey Pines last week, never looked like getting fully into his stride, despite an encouraging birdie at the third.
Bogeys at six and nine set him back and from there on in he was unable to get any momentum going in a tournament he has twice won.
"I just didn't hit it close enough. Didn't hit it well. Struggled with it and had a bad warm-up as well, and just one of those days," he said.
World number three Stenson moved ominously up the leaderboard as he recovered from a horror start to Thursday's opening round when he was three over after just five holes.
The big Swede had five birdies in his 67 that hoisted him up the leaderboard at seven under on a course he knows as well as anyone.
"I've played a lot of golf around here and you know where to go and where not to. There's not too many courses I know better that the Majlis," he said.
Three-time former winner Ernie Els was also in better nick with a 70, but at level par for the tournament, the South African was just outside the projected cut mark.
Leading scores on Friday in the second round of the $2.5 million Dubai Desert Classic, part of the European PGA Tour:-
Majlis Course, par-72
133 - Rory McIlroy (NIR) 63-70
134 - Brooks Koepka (USA) 69-65
136 - Damien McCrane (IRL), 66-70, Danny Willett (ENG) 71-65, Julien Quesne (FRA) 66-70
137 - Justin Walters (RSA) 69-68, Henrik Stenson (SWE) 70-67, Robert Rock 67-70 (ENG), Thongchai Jaidee (THA) 68-69, Edoardo Molinari (ITA) 65-72, Stephen Gallacher (SCO) 66-71, Jamie Donaldson (WAL) 69-68
138 - Morten Orum Madsen (DEN) 71-67, Francesco Molinari (ITA) 69-69, Emiliano Grillo (ARG) 71-67, Soren Hansen (DEN) 67-71, Roope Kakko (FIN) 69-69, Magnus Carlsson 69-69, Symon Dyson (ENG) 69-69
139 - Chris Doak (SCO) 71-68, Thorbjorn Olesen (DEN) 71-68, Kim Shi-Wan (KOR) 70-69, Joost Luiten 70-69, Brett Rumford 69-70, Jaco Van Zyl (RSA) 71-68, Gregory Boudry (FRA) 71-68 , Paul Lawrie (SCO) 68-71, Soren Kjledsen (DEN) 68-71, Richard Sterne (RSA) 66-73, Marcel Siem (GER) 72-67