One problem related to transmission noise has been reported for the 2006 Honda Civic. The most recently reported issues are listed below. Please also check out the statistics and reliability analysis of the 2006 Honda Civic based on all problems reported for the 2006 Civic.
Had the 3rd gear transmission problem fixed at 45,000 miles and since then it has always driven different. Kept going back to the dealership and told me there was nothing wrong with it. Now at 87,000 it got taken in to get the front fenders and hood re-painted because of the faulty manufacturer paint. The car started clicking before I took it in and when pressing the clutch noise would go away. They did an estimate for my throwout bearing and the next day they called me saying the vehicle would move at all, that I need it a new transmission. Now the dealership expects me to pay them $4,000 in total for labor and to put a new trans in the car. I have always had problems with this dealership and had a few complaints towards Honda. I also had the motor top gasket replaced because it was leaking oil and got covered under warranty since it was part of a recall.