Arsenal duo Robin van Persie and Laurent Koscielny will miss out after picking up hamstring and back injuries respectively.
Manager Arsene Wenger described the injuries as "short-term" and hopes the key duo will be fit for Sunday's Carling Cup final against Birmingham.
Johan Djourou missed the FA Cup draw with Leyton Orient with a back problem but is now fully fit and will start at the Emirates Stadium. Abou Diaby is suspended and long-term absentees Thomas Vermaelen (Achilles) and Lukasz Fabianski (shoulder) remain sidelined.
Stoke winger Matthew Etherington looks set to miss out due to a fresh injury concern.
Etherington shook off a hamstring strain to play in Saturday's 3-0 FA Cup fifth-round win over Brighton, only to be taken off with a back injury understood to be linked to a defect in his jawline.
Asmir Begovic will return in goal ahead of Thomas Sorensen, who has so far played in all the FA Cup ties, while Dean Whitehead is also due to figure after being rested as an unused substitute for the game with Albion.
Manager Tony Pulis only has two players definitely out injured in Mamady Sidibe (Achilles) and Abdoulaye Faye (hamstring).
Arsenal (from): Szczesny, Eboue, Clichy, Song, Djourou, Arshavin, Wilshere, Walcott, Bendtner, Chamakh, Fabregas, Nasri, Almunia, Rosicky, Sagna, Denilson, Squillaci, Gibbs.
Stoke (from): Begovic, Huth, Wilson, Delap, Etherington, Whitehead, Jones, Collins, Fuller, Pugh, Whelan, Pennant, Wilkinson, Walters, Carew, Shawcross, Higginbotham, Sorensen.