I just put new tail lights in my '03 3500 and found out that the brake lights including the third brake light aren't working. The trailer brake controller works and the trailer brakes work. What could be the problem?

 

Are they LED?

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Yes they are LED, but I put the old ones back in today, and still have no brake lights or 3rd brake light.

 

Here's where you use your multimeter to check circuits...Power where there's supposed to be power, grounds where there's supposed to be grounds......Ben

 

Betcha that somehow during the installation process you somehow managed to create a short. Pull the cover off the fuses and inside the cover you will see what fuses power what. Check or replace the fuse for lights that are not working.
Let us know what fixes the problem.

 

Fuses are all good.

 

Darn, lost that bet. Was hoping for your sake that it was something as simple as a blown fuse. As Fordzilla said, time to drag out that multimeter and start looking for where the voltage stops. Start by checking that there is power at the applicable fuse(s).