One player who will miss the tie is Bastian Schweinsteiger due to a suspension after picking up his third yellow card of the competition in the win at the Emirates.
Bayern are a top class side with numerous options available to them, which got us thinking about how strong an entire second string XI would be.
While the Gunners will unfortunately face a largely first choice selection of opponents, with Bayern likely to take no chances defending their two goal advantage, here is a second choice team Bayern theoretically could field - with no players included who featured at the Emirates.
Tom Starke (GK)
A reliable second choice who has played for Leverkusen and is a former German under-21 international. He has only played once for Bayern after signing last summer, but kept a clean sheet.
27-year-old Brazilian Rafinha doesn't get much of a look in because of the excellent Phillip Lahm, but he is a Brazilian international who has also played at the Olympic Games in 2008.
Jerome Boateng (CB)
Former Manchester City defender Jerome Boateng is usually a first choice, but was replaced by Daniel van Buyten at the Emirates so features here in our alternate XI. He has made 14 starts for the side this season at centre-back.
Holger Badstuber (CB)
German international Holder Badstuber didn't feature against Arsenal last time out either, and is normally a left-back, but has played four times at centre-half this season.
Diego Contento (LB)
Luis Gustavo (CM)
Brazilian midfield destroyer Luis Gustavo was linked with a £15 million move to Arsenal this week, and came off the bench at the Emirates on Tuesday night. The 25-year-old has two international caps to his name.
Anatoliy Tymoschuk (CM)
The 33-year-old midfielder has an incredible 125 caps for Ukraine and has made 10 Bundesliga appearances this season scoring once. He won the UEFA Cup with Zenit St Petersburg in 2008.
Xherdan Shaqiri (RM)
Swiss international Shaqiri has scored past England on two separate occasions and was instrumental in the Basel side which helped knock Manchester United out of the Champions League last season. He's still forcing his way into the Bayern side but is an exciting talent.
Arjen Robben (LM)
Dutch international Arjen Robben needs no introduction. The former Chelsea and Real Madrid man has been out of the side this season due to injury issues and the emergence of Toni Kroos, but still remains a devastating threat.
Mario Gomez (CF)
German international Mario Gomez had a sensational year last year, scoring 40 goals in all competitions for Bayern. He has suffered with injuries this year which has meant he has only scored five, losing his place to Mario Mandzukic, but at 27 he still has plenty to offer.
Claudio Pizarro (CF)
Former Chelsea forward Claudio Pizarro is the record overseas goalscorer in the Bundesliga. He signed for Bayern on a free last summer and has proved an able deputy, bagging a hat-trick in the Champions League demolition of Lille.
So what do you think, would Arsenal stand a chance against this team, or would Bayern still win?
image: © wonker