The 28-year old's contract expires at the end of June, and the official club website has indicated that the club are still in ongoing talks to secure the US international for another season, along with Andre Moritz and Arran Lee-Barrett.
This news shows remarkable faith in Holden, who failed to make a single appearance this season through injury. The midfielder first suffered a knee problem during a match against Manchester United in 2011, before returning to action six months later. This return was cut short as complications in his recovery caused a further 16 months on the touchline.
A return in 2013 signalled a potential change in fortunes, but on June 29 it was announced that Holden had torn his anterior cruciate ligament whilst playing for the United States in the CONCACAF Gold Cup final against Panama. This injury has kept him out for the majority of the 2013/14 season, and, whilst playing in a specially organised reserve match to assess his fitness in March 2014, Holden was injured once again - with a rumoured six-to-nine month recovery period.
On announcement of his most recent injury, manage Dougie Freedman told BBC Radio Manchester: "It is a shame for Stuart.
"The cruciate ligament popped again. He's disappointed and so are we all. It just seems to be where we are at with injuries at the moment."
This latest injury officially ends any hope of fighting for a spot in Jurgen Klinsmann's squad for the 2014 Brazil World Cup, with the midfielder unlikely to add to his 25 caps for the USMNT in the near future.
In the same article, Bolton also announced the list of players to be released when their contracts expire in the summer. Zat Knight, Chris Eagles, Tyrone Mears and Jay Lynch will the be the four players searching for new clubs come July 1.