Holden, 27, underwent scans on the injury he picked up in the first half of the USA's victory over Panama in the Gold Cup final on Sunday evening.
Those scans have subsequently revealed the midfielder will miss a considerable period of time again after lengthy spells out with knee problems in 2011 and 2012.
"We've got the scans and the results will be analysed by our specialists," head of sports performance Mark Leather told Bolton's official website. "We can then put an action plan in place over the next week to 10 days when the initial swelling reduces."
Holden's first serious knee injury with the Trotters came in March 2011 following a tackle from Manchester United's Jonny Evans.
He made his comeback in September of that year against Aston Villa but had to have a follow-up operation and would not appear in a Bolton shirt again until January 2013.
Holden returned to the international stage in May after a two-year absence and United States head coach Jurgen Klinsmann told ussoccer.com: "We are absolutely devastated for Stuart.
"He was fully prepared to head back to Bolton and challenge for a starting spot. Now he will have our full support as he goes down this road again, and we will be with him every step of the way."
Speaking on Twitter, Holden himself added: "I will rise again! Big love and thanks to all."