One problem related to manifold/header/muffler/tail pipe has been reported for the 2006 Hyundai Sonata. The most recently reported issues are listed below. Please also check out the statistics and reliability analysis of the 2006 Hyundai Sonata based on all problems reported for the 2006 Sonata.
I purchased a 2006 Hyundai Sonata in October 2005. The vehicle has developed a high pitched whine at 60-69 mph (2,000 rpm). I have taken the vehicle to my Hyundai dealership and they have been informed by Hyundai engineers that the noise comes from a design flaw dealing with the variable intake manifold. They are apparently aware of this matter but are doing nothing to rectify it. The noise is loud enough and high pitched enough that it could and does cause a driving distraction.