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I usually refer to it as a "he"

Due to Skeletron spawning from the Old Man/Clothier, most people refer to Skeletron as a he.

Also, congrats!

I mean, they don't have much from the shoulder down, so I don't think they have one. Whatever floats your boat though, and it's not like they care about much besides removing your limbs, so don't sweat it.

What is your gender?
Male
Female
Flying Skeleton Skull with Arms

A HELICOPTER!