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2 weeks ago while driving to work I noticed my transmission started having a hard time shifting into 2nd gear. When I first turn on the car, it drives great. About 5-10 minutes after driving, it will start having trouble shifting into second gear. After a while it completely stops working. If I shut it off for a while, it starts working again until warm. Would this mean the transmission is going out?

 
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01 02 03 were the years that were known for automatic transmissions failures. It happen to my 2001 civic as well but I got lucky as it didn't stop working it was still working with issues so I replace it at the dealer with brand new one. Your best bet would be to either replace it with a junk yard one or any transmission guys could do it as well. Hope this help.