Earlier Friday, O'Neill told the Dan Patrick Show that I'll Have Another was out, citing an injury to the horse's left front leg.
"I'll Have Another is officially out of the Belmont," O'Neill told the radio show. "He galloped great yesterday, and in the afternoon he had a little bit of swelling in his left front leg.
"This morning, he looked perfect. I took him out and I just did a little something with him. After training, that swelling came back.
"I had the vet come over. He scanned his left front leg. He's got the start of tendinitis going on in that front leg, so he's not 100%. And we ain't taking any chances."
O'Neill told the show that he didn't know how the horse became injured.
"Pulling him out, it's not tragic, but it's a huge disappointment. (I'm) just so disappointed for the horse, obviously, and ... the whole team.