That ended his tournament and he has not yet featured for Edinburgh in the GUINNESS PRO12 since his return.
And Edinburgh boss Alan Solomons has revealed that Gilchrist required surgery on the problem and is now looking at a number of months on the sidelines.
"It's difficult to tell with these things but we're talking months not weeks," he said.
"You try to deal with the thing conservatively but we got to the stage where it was felt by the specialist that it was best to operate.
"He's a little bit uncomfortable and on crutches but we have a great medical team here and they'll get him back as soon as they can."
It's been a rough year for Gilchrist, who broke his arm shortly after being named Scotland captain, and has not featured for Edinburgh in the GUINNESS PRO12 since October 2014.
This injury will see him miss an extended period, and could also cost him a chance of being involved in Scotland's Six Nations challenge.
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