One problem related to automatic transmission has been reported for the 1999 Toyota 4Runner. The most recently reported issues are listed below.
1999 Toyota 4runner, the left rear wheel axle seal is leaking gear oil all over the left rear wheel and brake. I have had the rear axle seals replaced 5 - 7 times: December 2006, June 2007, December 2007, June 2008, December 2008, and now again it is leaking February 2010. The independent auto repair business where I take my vehicle subscribes to "all data which assists mechanics all over the country in sharing work done on vehicles; assisting in diagnosing similar problems, etc. There are a tremendous number of similar left rear axle seal failures on Toyota 4-runners and pickups 1999 - 2001 which use the same axle listed in the all data web site. Many of these list multiple times the seal as failed on the same vehicle. . I my case we have been getting the seals from Toyota. The rear brake on the left side is covered in axle grease which in my opinion will seriously limit my braking ability and could contribute to and accident. I was not able to stop and rear ended another vehicle in the summer of 2007. Fortunately no one was injured in this accident.