"One of [Train's] parents was born a hermaphrodite, and [their parents] cut off the penis. His/her whole life, this person wanted to be acknowledged as a man. The parents wanted the child to not be identified as a boy or a girl, and the child didn't really have a name --one week it's Tigger, another it's Train. Many years ago I wrote it down, and I always wanted to write a song called 'Little Boy Named Train.' [This] happened to someone else, but there's a part of me I was thinking about when I wrote it. There's a line: 'I'm always lost, I'll never change, give me directions and I'll get lost again.' Kind of autobiographical." -- Billie Joe

Billie Joe's son went to school with "Train". Throughout the song, the narrator alludes to the general feeling of uncertainty surrounding this character. As a child, the character did not have control of his life, and was forced to roll with the punches, "like a rat inside a maze." This carries strong meaning, because this high degree of uncertainty isn't usually part of a person's life. Now, the only choice "Train" has is to accept what he's been through, and wonder where he'll be tomorrow. The song is completely summed up in these lines: "Don't know where I come from / But I know where I have been."