Also included in the 27-man squad is Mick O'Driscoll who missed last Sunday's league game in Cardiff with an ankle injury.
Earls (groin) and Flannery (calf) both played in the Heineken Cup semi-final loss to Biarritz Olympique, but Howlett (hamstring) has been out of action since the quarter-final win over Northampton Saints.
The players are being given every chance to prove their fitness for Saturday's interprovincial derby in which Munster will hope to put a three-match losing streak against Leinster behind them.
That losing run includes last season's Heineken Cup semi-final defeat (25-6) and home and away reversals in the Magners League in October (30-0) and last month (16-15).
That one-point loss in Cork was a game that could have gone either way, with a converted try on the cusp of half-time by Rob Kearney proving crucial for Leinster.
"Leinster really pinned us in our own half in the last 20 minutes (of that game) and put us under an immense amount of pressure," explained Munster coach Tony McGahan.
"There wasn't much in it with a bounce try to separate the sides. I think the kicking game is going to be a huge part of this weekend's game.
"Leinster have demonstrated this season and last that they have great physicality in attack and defence and that's going to be a crucial area for us as well.
"We have only, on limited occasions, managed to gel everything together."
Giving the players' viewpoint, full-back/winger Denis Hurley is clearly relishing this chance to put one over on the table toppers.
"I'd say we're pretty optimistic, and probably refreshed now that we've made the Magners League semi-final," said Hurley, who played on the right wing against Cardiff.
"We're glad to have the opportunity to play Leinster again as well. I suppose the way the season has gone we haven't really performed to a level we would have liked against the home provinces, Connacht excepted.
"So this is an opportunity to maybe put that to bed before the end of the season. It's an opportunity, nothing more. But one we're looking forward to.
"Games between ourselves and Leinster are always battles and we haven't been on the front foot in recent times. From game to game, when we do meet, anything can happen and that's the way we have to approach it this weekend again."
MUNSTER Squad (v Leinster) - Backs (12): Scott Deasy, Danny Barnes, Denis Hurley, Doug Howlett, Tom Gleeson, Keith Earls, Lifeimi Mafi, Jean de Villiers, Paul Warwick, Ronan O'Gara, Peter Stringer, Tomas O'Leary.
Forwards (15): Marcus Horan, Dave Ryan, John Hayes, Tony Buckley, Jerry Flannery, Damien Varley, Denis Fogarty, Donncha O'Callaghan, Mick O'Driscoll, Billy Holland, Alan Quinlan, David Wallace, Niall Ronan, Nick Williams, James Coughlan.