The France international underwent surgery to remove a tumour on his liver in March last year but returned to the first team and had the honour of lifting the Champions League trophy at Wembley in May.
However, Barcelona have now said that Abidal will be forced to have a transplant - a course of action that has been under consideration for 12 months.
A club statement read: "Given the development of his medical condition, Abidal will undergo a liver transplant in the following weeks.
"The transplant is an option that has been considered since the beginning of his treatment, one year ago.
"At the express wish of the player, the club request the utmost respect for the right to privacy and confidentiality."
Abidal has started 32 games in all competitions for Barcelona this season.
The club did not say how long the 32-year-old would be out of action but his chances of returning before the end of the season and representing France at Euro 2012 starting in June must be in serious doubt.
Abidal's Barca team-mates rallied behind him following the announcement, with striker David Villa, himself sidelined with a broken leg, saying they needed him back in the team as soon as possible.
"All my strength for Abidal!" Villa wrote on his Twitter feed. "You will get through it. You are very strong. We will all be by your side," he added.
Central defender Gerard Pique wrote on his feed: "You will return and you will do it like always, being the best! You are an example for everyone."
Barca are losing Abidal at a critical time in the season, with the Champions League holders through to the quarter-finals of Europe's elite club competition and bidding to close a 10-point gap with Real Madrid in La Liga.
They are also will face Athletic Bilbao in May's Copa del Rey final.
Abidal is likely to be replaced in Barcelona's line-up by Adriano and captain Carles Puyol is also able to fill in at left back.