The 33-year-old did recover from that calf injury but subsequently suffered a back problem that despite exhaustive and thorough medical treatment forced his decision.
He joined Munster from Connacht at the start of the 2003/04 season and broke into the Heineken Cup squad in the 2005/06 campaign, playing in all nine games in Munster's run to the title.
Injury confined his Heineken Cup appearances to three the following season but he was once again a central figure during the 2007/08 season as Munster captured the European crown for a second time.
In addition to the 94 caps the hooker won with Munster, he was capped 41 times by Ireland, starting in four of their five games during the 2009 Grand Slam campaign.
Later that year he was selected for the British & Irish Lions tour to South Africa only to be forced to withdraw when he fractured his elbow at the training camp in England.
"I'm very sad to have to announce my immediate retirement from rugby due to injury," admitted Flannery after the news had been announced this morning in the University of Limerick.
"Since my injury at the 2011 World Cup, I've struggled to regain the level of fitness required to play at this level and after consulting with the Munster and Ireland medical staff, I am announcing my retirement with immediate effect.
"I would like to thank all the medical staff who have worked so hard on my behalf and shown great patience in dealing with me.
"I'm incredibly grateful for all the opportunities rugby has given me to date and i would like to thank all my friends, family, coaches and team-mates for their support along the way.
"Finally I would like to thank all the Munster and Irish rugby fans who I have been so proud to represent over the course of my career. Your level of support has been amazing and I can never thank you all enough. It's been emotional!"
Commenting on the news, Munster Chief Executive Garrett Fitzgerald said: "I have known Jerry since his time playing rugby with St. Munchin's. At that stage, he was identified as a future Munster and Ireland player and he has delivered in no uncertain manner.
"His attitude and approach always meant that he was destined for success as was proven with his selection for the Lions in 2009, his contribution to Ireland's 2009 Grand Slam success and winning two Heineken Cup medals with Munster.
"An example to all young players in what hard work and dedication can achieve and more so in how he has remained positive through adversity when it would have been easy to seek pity.
"I know he will continue to contribute to rugby in Munster and I wish him well in his future career and business."
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