One problem related to tailgate has been reported for the 2006 Toyota 4Runner. The most recently reported issues are listed below. Please also check out the statistics and reliability analysis of the 2006 Toyota 4Runner based on all problems reported for the 2006 4Runner.
In September 2012 I noticed paint blistering on the tailgate of my 4runner. I now (8/13) have rust through originating from the inside middle of the tail gate. I took the truck to my local body shop and was told that this was a common problem with the 06 4runner. It was caused by a sound deafening material on the inside of the gate. "the material gets wet and holds the moisture causing body rot". This shop has repaired other 4runners with this problem. I also own a 1994 isuzu trooper with no body rust that sits next to it in my driveway. I was told by the Toyota rep (oakdale Toyota in NY) that it was out of warranty and they could not help me. I also have extensive rust on the undercarriage. The truck has never been off road before.