The bolts attaching the front door window glass to the window regulator may come loose. This can cause the window regulator to become damaged and possibly causing the window glass to break. Some 2003 & 2004 models have been recalled for the issue.Google+
Car Problem Reports
Toyota Matrix Bolts That Attach Front Window Glass to Window Regulator May Fail
Toyota Matrix Problem
Average Mileage: 91,197 mi (35,000 mi - 123,778 mi)
Visitor, 2005 Toyota Matrix, 94,000 mi
The glass of the passenger side door fell inside the door and the motor will not bring the window up nor put it down. The glass is not broken and is inside the door
Visitor, 2006 Toyota Matrix, 60,000 mi
Have similar problems to those reported already. About 2 years ago driver's side rear door power window stopped operating. My mechanic tested it and diagnosed as electric driver motor failure. Now, just before Christmas (2012) driver's side window almost broke when it came out of track and it does not close anymore. It had to happen of course when it was -20C outside and snowing. This problem had a recall made by Toyota but only for 2003 and 2004 years of make. Our dealer (Country Hills Toyota of Calgary)said we have to pay $139 diagnostic fee before they even start fixing it. How ridiculous!! I told them to go to hell course they knew exactly what's wrong with it based on info from previous years of Matrix affected by the recall. I phoned different dealer and they knew right away what was the problem and that they would fix it for $129 without any diagnostic involved. Thinking about doing it myself or making appointment with the second phoned dealership (Charlesglen Toyota of Calgary)
Visitor, 2006 Toyota Matrix, 123,778 mi
Passenger side window drops down half way and then bolts catch making a loud noise. Only when window goes down, not up.
Visitor, 2003 Toyota Matrix
also back windows won't open - fixed then back to problem within one yr.
Visitor, 2006 Toyota Matrix, 110,000 mi
Driver's window started making clunk part way up when closing. Then window almost came out
of track with top rear corner lifting out of frame. Was able to guide window back and have not used since.
Now, my girlfriend's 2003 made a loud clunk on closing. Suspect the same problem.
Will be opening door panel to check mine.
Driver side window slipped down and the regulator had to be replaces at cost of $200 last year.
Then this week the passenger window completely fell into the door! I plan to go to a dealer and request a free repair.
My rear driver's side window will not roll. neither the switch on the driver's door nor the one on the rear driver's side door will work to roll the window. I cannot even hear the motor try to make an effort.