All three suspects face several charges, including conspiracy and trafficking.
The alleged car-cloning cells have been in operation for at least five years. More than 1,000 cars have been stolen.
The FBI says consumers aren't likely to realize if they've bought a stolen car.
"What's called the public VIN, or the publicly observed vehicle identification tag, has been altered or changed so it reflects the real vehicle, and the supporting documentation, the bill of sale, the title, has also been changed to match the tag that's on the car," said Ross Rice, FBI spokesperson.
The FBI says, in the Chicago area, there are more than 100 victims who have bought cloned cars and don't know it.