Flannery injured a knee in the GUINNESS Series match against Argentina but has staged a remarkable recovery to regain his place in the starting side.
Munster completed their match preparations at the University of Limerick on Wednesday and while Flannery took a full part, Barry Murphy sat out the afternoon session because of a slight back problem.
But Murphy's absence was purely precautionary and the UL Bohemians clubman is fit and and ready to take his place alongside Lifeimi Mafi in the Munster midfield.
MUNSTER (v Clermont Auvergne): Keith Earls; Doug Howlett, Barry Murphy, Lifeimi Mafi, Ian Dowling; Ronan O'Gara, Tomas O'Leary; Marcus Horan, Jerry Flannery, John Hayes, Donncha O'Callaghan, Paul O'Connell (capt), Alan Quinlan, Niall Ronan, David Wallace.
Replacements: Denis Fogarty, Tony Buckley, Donnacha Ryan, James Coughlan, Peter Stringer, Paul Warwick, Kieran Lewis.