One problem related to differential unit has been reported for the 2006 Toyota Sienna. The most recently reported issues are listed below. Please also check out the statistics and reliability analysis of the 2006 Toyota Sienna based on all problems reported for the 2006 Sienna.
I have a 2006 Toyota Sienna le with automatic transmission that is currently at 76256 miles. I had bought it new. (delivery date 1-Jan-2007) on 20-Dec-2012, at 75800 miles, I noticed a whirring sound (like a turbo whine) when I lifted my foot off the gas (no load) around 45 mph. The grinding/whirring noise would be most apparent between 25 mph to 45 mph. I took it to my nearest Toyota dealership on 31-Dec-2012 for checkup ( 76257 miles at the time) and they diagnosed that the transmission was going bad and will need to be replaced. The exact diagnosis was that the "side carrier bearing inside of the differential is making the noise. Need new transmission - $5700. 00". The estimated cost is $5700. 00 this looks like a design flaw in the transmission, I am the original owner and have driven the van with lot of care. It is unacceptable that the Toyota transmission would start to fail at less that 76000 miles. I had bought a Toyota van assuming that their vehicles are reliable. I believe there are many 2006 Toyota Siennas on the road that will start having this problem. This can cause a hazardous situation if the transmission fails on a highway causing an accident. Toyota should provide extended warranty for the Sienna transmission just like they did for rav4 2001-2003 model when they extended that warranty to 10 years or 150,000 miles.