Reyes could be partnered either by 19-year-old David Bentley or 17-year-old Quincy Owusu-Abeyie.
While captain Patrick Vieira, who was suspended against City on Sunday, is certain to be there tonight to lead by example, Fredrik Ljungberg is doubtful with a rib injury and Robert Pires may not be risked.
There are fears that Ljungberg may be out for three weeks with a cracked rib sustained in the match against City.
The Swede said: "I was hit by a City player and it hurt like hell. One of their players ran straight into me and hit me in the ribs. It is impossible for me to keep on playing. On Sunday night the pain was so bad that I needed to take painkillers to enable me to sleep."
Ljungberg's absence could at least leave Gilberto Silva and Ray Parlour to strengthen the midfield, but Jens Lehmann, Sol Campbell and Ashley Cole should also be rested.
Wenger declared: "We'll look to the likes of Reyes, Pascal Cygan, Bentley, Edu, Patrick Vieira and maybe one other player who started against Manchester City.
"That was a very physical game and I have to protect the squad as we have many big games coming up and it'd be dangerous to expose the players in this match.
"If I put all the first-team players out this Tuesday night, they will not survive after that, I can guarantee you. It's impossible for me to do it."
Cygan, 29, will have an important part to play in Arsenal's attempt to pull back their one-goal deficit.
Nobody has been more delighted with Cygan's progress than Wenger. He saw how the player suffered when he first arrived at the club following his £3m move from Lille. He said: "In his first season there were many doubts about him. He has now given the answer.
"He is an intelligent boy and he worked hard. At first he was not convinced that he had his place here but I always told him I had faith in him.
Boro are awaiting fitness reports on Gareth Southgate (hamstring) and Ugo Ehiogu (groin strain).
Middlesbro (1) v Arsenal (0), Riverside Stadium, tonight, 8pm. Live on Sky Sports 2
