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Q: how do i program my spare key on 2004 Honda Civic

When I bought my Civic I received two sets of keys. Only one will start the car. The other works on everything except ignition
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You car is still under warranty, right?

This is something that the dealership should fix for you under warranty. It sounds like a problem to me.
That's not good news--makes it a little more complicated and probably expensive. I'm not sure that anyone but the dealership can help with programming keys.

I would give your local Honda dealer a try and tell them it never worked correctly. If the price is too high, perhaps a local Honda specialist can help with it. Replacing keys can be well over a hundred dollars. With luck, that won't be necessary!
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