Munster were the only team to go through the Heineken Cup Pool stages unbeaten and as well as O'Connell there have also been injury doubts surrounding scrum half Conor Murray and lock Donnacha Ryan.
"News of injured trio Paul O'Connell, Donnacha Ryan and Conor Murray is positive. Ryan took a limited part in training yesterday, while O'Connell and Murray travelled to Dublin to see a specialist who cleared them for training next week," said a Munster spokesman.
"Ryan would look to be on track for inclusion in the squad for the Heineken Cup quarter-final against Ulster, while O'Connell and Murray's participation will depend on how they come through training."
All three will miss Saturday's night's top of the RaboDirect PRO12 shoot-out with Leinster Rugby at Thomond Park. Ronan O'Gara will lead the side and head coach Tony McGahan also welcomes back three other Irish internationals in Keith Earls, Donncha O'Callaghan and Peter O'Mahony
Munster: Felix Jones; Johne Murphy, Keith Earls, Liefemi Mafi, Simon Zebo; Ronan O'Gara (captain), Tomas O'Leary; Marcus Horan, Damien Varley, BJ Botha; Donncha O'Callaghan, Mick O'Driscoll; Dave O'Callaghan, Peter O'Mahony, James Coughlan
Replacements: Mick Sherry, Wian du Preez, Steve Archer, Billy Holland, Tommy O'Donnell, Duncan Williams, Ian Keatley, Danny Barnes.