The Irish golfer traced the condition back to a bad viral infection he had 18 months ago in China, leading to some scar tissue and the thickening of his left ventricle.
The four-time major victor revealed the heart "irregularity" in an interview with a British newspaper published on Friday.
McIlroy, 28, missed a large portion of the 2017 season with a rib injury and as a result slipped from No 2 in the world rankings to No 11 and failed to win a title.
"I've got a bit of an irregularity with my heart that I have to keep on top of", McIlroy told the Telegraph. "For now, I just need to stay on top of it and have to stay fit", the Northern Irishman told the newspaper.
"Yesterday, I did an interview with the Daily Telegraph where I spoke about a range of topics regarding the last three months of my life", McIlroy wrote.
McIlroy is set to play in next week's Abu Dhabi Championship in Dubai, his first tournament since shutting down his game in October to deal with a fractured rib.
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"I think about number of wins, the ability of the players against me, the number of majors the others have. I'm not hung up on it". "I need to get back on that track and this year my goals are to add to my major tally and get back to World No. 1, winning more times than anyone else".
It is, after all, a statistics-dominated sport.
FILE - In this August 12, 2017, file photo, Rory McIlroy watches his tee shot on the third hole during the third round of the PGA Championship golf tournament at the Quail Hollow Club in Charlotte, N.C. McIlroy says he has a heart ailment that will have to be monitored regularly but is not expected to affect his play.
But when it came to "strokes gained putting" he found himself a lowly 140th on the list.
The constant tinkering was perhaps an inevitable legacy of Nike's abrupt dissolution of its golf equipment interests a year ago.
McIlroy said the irregularity stems from a virus he got in 2016.