With a ten to twelve week recovery time he will miss his side's remaining two European pool fixtures against Castres on Friday January 14 and the trip to Murrayfield to face Edinburgh the following weekend.
"Gethin went to see the specialist late last week and the recommendation was to have an operation on his toe," said Blues director of rugby Dai Young.
"The toe has caused him a problem for about twelve months now so he's booked in to have an operation on Wednesday that would mean he's out from ten to twelve weeks, which will mean he will miss the Six Nations, which is a big blow for Wales and for us."
"The hope was that with reduced training and with rest the toe would heal itself. They've gone down every path because Gethin wanted to avoid the operation if he could but it's at the stage now where the only option was to operate."
"The toe injury has affected his calf and Gethin feels he hasn't played the way he'd like to because he hasn't done the fitness training that he normally does."