Yes, but ONLY in full-season leagues - there are no injuries (or fatigue) in the exhibition season leagues. Guys can go down for a play and come right back or be out for 1 or more games. If a player is injured in the game, it will be highlighted in RED in the play by play. If he can not return to action in the current game, his injury status will be displayed in your coach's office next to his name. In addition to the injury, you'll also see the number of games until he will return. Until he is cleared to return to action, the player will be unavailable to play. Any injuries suffered during pre-season games will be eliminated when the regular season begins.
NOTE: If you have no available healthy quarterbacks or not enough skilled position players, you will forfeit the game. Either call someone up from your practice squad or waive an injured player and pickup a healthy one off the waiver wire.