The Blues defender has spent the last three months on loan at the League One side.
"I'd like to thank Sam for his efforts during his time here, because although he may not have got as much pitch time as he would have liked, he has been an important part of the squad," Orient boss Martin Ling told his club's official website.
Defender Back From Loan Spell
"The rules state that he must go back to Birmingham now, but we will look at the situation again when the January transfer window opens."