I was working on a furnace which uses 120v and the control circuit uses 24v. I checked the two secondary leads on the transformer and got 0v. Then I checked the primary hot lead and the chassis and got 120v. Turns out the primary neutral had a bad connection. My question is when I checked either secondary lead (without the primary neutral connected) to the chassis i got 12v. How could I get anything when there is no current flow through the primary side of the transformer? Thanks

ds247,
By rights, you shouldn't have had 12V to the Chassis (unless one side of the Secondary is connected to it).
Assuming that this is a Double-wound transformer, there should only be voltage between the two secondary leads.
It sounds like there is a broken turn on the Secondary side of the transformer.

This could be capacitive coupling across the transformer and returning over the chassis to the 120v ground. Or if the neutral is broken in a way that allows it to capacitively couple with a ground wire, it could be a complete circuit through that coupling. Put a 24v load on the secondary (a pigtail socket with a 100w 120v light might do). If the former cause, the 12v may remain. If the latter cause, it should go away.