CORK, June 20, 2014 (AFP) - The double Major winner produced a roller-coaster second round of a two under par 69 to fall one shot shy of playing all four rounds on the Fota Island Resort course.
It is the second Irish Open in succession McIlroy has missed the cut and he will now have a fortnight off, including practice rounds at Royal Liverpool and venue for the year's third Major, before teeing up next in the July 10th Scottish Open at Royal Aberdeen.
McIlroy went into the second round sharing 125th place and while he got off to a bright start with a third hole birdie he was struggling when his tee shot at the par four fourth hole ricocheted off a tree and over an out-of-bounds fence and into the adjoining Fota Island Wildlife Park.
The current World No. 6 walked off the hole with a double bogey.
McIlroy made amends with back-to-back birdies at five and six but he also had back-to-back bogeys at eight and nine before the highlight of his round in holing a four-foot eagle putt at the 10th.
He was still three shots shy of the projected cut-off mark with two holes to play and needing to play them in three under but while he drew huge applause the pair of birdies was not good enough.
"It's disappointing not to be able to in front of such a big crowd over the weekend, but I also feel more so for them a little bit," he said.
"It isn't what I want to happen when I come back home to play.
"But I'll be back next year and try and do better.
"And when I look back at every Irish Open I've played, I definitely can't say that I have played to my potential. Definitely not. Not even close. Not even close.
"I'd love to be able to produce my best when I come back home, and it hasn't been this year or last year of the previous years, but hopefully I'll start to in the future."
Finland's Mikko Ilonen maintained his lead on the field adding a two under par 68 to his opening round new course record of 64 to move to 10-under par.
The 34-year old Ilonen birdied his opening hole but then stalled with eight straight pars ahead of an inward half of two under that included four birdies and half as many bogeys.
"I got to my goal and that was to get to double digits, so I wanted to at least get to 10-under par and I did that," he said.
"It wasn't as easy today and I didn't hit the ball that well but I putted well and it was good enough."
Three players, former U.S Open champion Graeme McDowell of Northern Ireland (66), England's Robert Rock (66) and Frenchman Romain Wattel (65) share second place on eight under par.
McDowell is looking to win the Irish Open for a first occasion in his career while Rock has been runner-up twice before including losing out in a play-off to Ireland's then amateur Shane Lowry in 2009.
Leading scores after the second round of the Irish Open at par-71 Fota Island course on Thursday:
132 - Mikko Ilonen (FIN) 64 68
134 - Robert Rock 68 66, Romain Wattel (FRA) 69 65, Graeme McDowell 68 66
135 - Marco Crespi (ITA) 68 67, Matthew Nixon 70 65, Simon Khan 69 66
136 - Sihwan Kim (NOR) 69 67, Gareth Maybin 71 65, Edoardo Molinari (ITA) 67 69, Padraig Harrington 69 67
137 - Roope Kakko (FIN) 71 66, Magnus A Carlsson (SWE) 66 71, Anders Hansen (DEN) 67 70, Gary Stal (FRA) 70 67
138 - Chris Wood 69 69, Adam Gee 68 70, Kristoffer Broberg (SWE) 69 69, Matthew Baldwin 67 71, Stuart Manley 70 68, Daan Huizing (NED) 67 71, Paul Casey 69 69, Andrew McArthur 71 67, (x) Gary Hurley 72 66, Gregory Havret (FRA) 70 68
139 - Daniel Willett 73 66, David Howell 72 67, Graeme Storm 69 70, Ricardo Gonzalez (ARG) 69 70, Fabrizio Zanotti (PAR) 70 69, Gregory Bourdy (FRA) 68 71, Christopher Doak 69 70, Michael Hoey 68 71
140 - Steve Webster 70 70, Ross Fisher 68 72, Estanislao Goya (ARG) 70 70, Marcel Siem (Ger) 66 74, Tom Lewis 68 72, Darren Clarke 72 68, Alvaro Quiros (Spa) 70