Wes Brown, Sol Campbell and Alan Smith sat out England training on Tuesday.
Brown was left back at the team hotel nursing a knee injury that kept him out of Manchester United's 4-0 win over Wigan.
Campbell and Smith were receiving treatment at England's St Albans training base, for Achilles and knee problems respectively.
The remainder of Steve McClaren's 25-man squad were in attendance, meaning Michael Owen and Frank Lampard both trained.
Owen had hernia surgery just last week but came through a cameo appearance for Newcastle at the weekend unscathed.
Lampard, meanwhile, played the full 90 minutes for Chelsea at Bolton on Sunday after sitting out all of September with a thigh injury.
England captain John Terry, who also faced Bolton as well as Valencia in midweek, was wearing his protective mask.
McClaren's men welcome Estonia to Wembley on Saturday before travelling to Moscow for a crucial Group E clash against Russia four days later.