See http://www.punchwood.com/index.php?/topic/21789-iron-golem-despawn-zombie-siege/

Brief: I have a village that started with about 10 villagers. Two iron golems spawned for them (many buildings/doors). I killed a couple villagers (passively, no aggro) to get new ones to spawn for better trades. So that left around 8. I left town for a while and came back and one of the golems was gone. The town is completely surrounded by two fences with no way to jump over, and it's lit up like a Christmas tree.

With no way in or out and no damage from a creeper evident, the golem is just gone. Despawned? Don't think so.

Is there any way to find out what happened to it? I don't know if it somehow disappeared "naturally", was killed, or if there's a glitch somewhere. I have a snapshot of the world from a couple days ago. I could replay but certainly can't reproduce everything exactly. Happy to help with diagnostics.