Emotionless was found to be suffering with a knee injury after his disappointing run in the Dubai Dewhurst Stakes at Newmarket.
Godolphin's big hope was the chief market rival to eventual winner Air Force Blue but crossed the line in last place having been eased down by William Buick.
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Subsequent X-rays revealed a chip in his left fore knee, but trainer Charlie Appleby is confident Emotionless will make a "full recovery".
"Following his disappointing run in the Dewhurst Stakes yesterday, Emotionless was found to be lame this morning in his box. He was immediately X-rayed and a chip was identified in his left fore knee," Appleby told www.godolphin.com
"I understand that its removal will not be a complicated procedure and we expect him to make a full recovery.
"We will be looking towards the trials in the spring, all being well."
