Which parts fail
Components named in complaints (automatic and manual transmissions, CVT, axles, driveshaft, 4WD/AWD).
Mileage when the problem started
Owner reports
Selected complaints filed with NHTSA by 2004 Toyota Matrix owners, lightly cleaned up (personal details are redacted by NHTSA).
Dt: 2004 Toyota Matrix xr, the vehicle has a problem with the steering, there was a noise coming from the steering yoke, consumer states the steering did not feel right, the consumer had taken the vehicle to the dealer to be repaired, the dealer told the consumer that the problem was because the splash guard was dragging, the dealer put two pins in the splash guard, because the pins were missing, the consumer took the vehicle to the dealership again to be repaired, the dealer told the consumer that the problem is with the steering yoke, previously the transmission had went out on the vehicle, the transmission seemed to have a loud noise coming from it. The consumer took it to the dealer. There was damage to the case and the dealership replaced the transmission because the vehicle was still under warranty. The vehicle is currently at the dealership waiting for a yoke replacement. …
My 2004 Toyota Matrix xr with manual transmission has suddenly displayed severe mechanical noise from the engine/transmission area. Smog technicians wouldn't take liability to run engine for smog tests to register for the coming year, so is now registered as planned non-operation until I can get the car fixed. Googling "Toyota Matrix transmission noise" or "Toyota Matrix engine noise" leads to several sites in which too many owners are either experiencing complete engine loss due to "oil sludge problem" or total transmission loss due to "admitted transmission bearing design flaw". I will not drive this car again on the roadway due to the possibility of sudden and complete loss of transmission function at any time. …
I purchased the vehicle used in 2007 with 15,000 miles on it. Within a year the transmission went out. Got this repaired by the dealership and within a year the transmission went out again. I have been doing research on this model year Matrix to see if it was just my car doing this, but it looks like there have been other people with 2004 Matrix that have the same problem. What happens is parts of the fly wheel or clutch dysfunction. It makes the car stop and it makes a grinding noise. It happened once while I was on a remote section of highway and the other time I was starting my car in the morning to leave for work. My car has close to 70,000 miles on it now, but as I stated previously, it happened at around 20,000 miles the first time, which is unusual for a Toyota, or any car for that matter. …
I have a 2004 Matrix (5 speed manual) with 85K and the throwout bearing has failed. I was driving home from a concert with a few youth kids on Saturday night. I was entering the 1-10e trying to merge in with traffic when the throwout bearing failed. I tried to shift into 3rd gear, but it was stuck in 2nd. I had to slam the gear into place to prevent getting run over by a SUV. This was my second near-death experience this year in my car due to the transmission. Earlier, when the car was at 74K, the front axle on the transmission broke. This broke in the middle of a busy intersection where I had to keep swaying my body forward until the car had enough momentum to roll across. After replacing the front axle, I really do not have the money to fix another transmission issue. …
Low noise from engine area, then heard a pop or thud. After this came a scratchy/grinding noise when car was in gear and coasting. The noise went away when clutch was depressed or car was taken out of gear to coast. I called a service repair to make an appointment the same day. The very next day the car locked up and was undriveable. Sounded like the engine had fallen out the bottom with horrible metal grinding noise. I had to have it towed ($150) and the service center said I would need a new transmission and clutch and that this is a common problem with Toyota Matrix and corolla. After reading online, it seems there is a problem with Toyota owners with low miles having bearing issues and that this problem has gone unaddressed. Even though I was going only 10 miles per hour, the car locks up. This issue will kill someone, someday. Cost of repair will be around $3,100+.
While on the highway, our 2004 Toyota Matrix, approx. 98K miles started to buck and make a terrible grinding noise. We then lost 4th and 5th gears. We were fortunate to be able to take control of the vehicle and get to the side however we were stuck at night on the highway. The transmission bearings shredded causing the clutch to fail. Replacement cost $3500.00. Since, we had read about hundreds of other similar complaints about this vehicle and were shocked that Toyota has not accepted responsibility for inferior parts and recalled the transmission. Toyota's reputation and thought of dependability and safety has faltered. It is sad because we have owned several other Toyota's in the past but will not consider purchasing another. We feel we were put knowingly into danger driving this vehicle as so many others unfortunately shared the same experience with same model/yr Toyota.
2004 Matrix transmission failed while wife was driving on highway on a rainy night. Prior to this the transmission began to have noises which one might attribute to an auto at 110,000 miles. After this failure transmission would not shift except with great difficulty. I had the Matrix towed home and am in the process of determining solution. The rest of the car is flawless but this early failure of a manual transmission in a Toyota is discouraging. The situation was a dangerous one as failure of the transmission caused those vehicles around her to become aggressive towards the slowly moving Matrix. My wife was extremely fortunate to coax the car to safety. These unexpected repairs will cost me around $2500 to $3000 to resolve. The auto is of no value without the repair, and with the repair resale not much greater.
Clutch failure at 5100 miles; --- complete-- replaced by dealer at 8600 miles---- clutch failure. Dealer refuses to deal with warranty. Tells me that it is my fault, " I don't know how to drive a manual transmission". Indicates that my wife and I are "riding" the clutch and perhaps "racing" mentioned vehicle. After a combined driving experience of nearly 3/4 of century on driving manual transmissions with zero problems, I seriously doubt that the cause of my clutch failures are my driving abilities or habits. Dealer service mentions that there is no evidence of history of complaints against this particular vehicle. Instead wishes to pass the "blame" and cause onto the customer.
Tl contact owns a 2004 Toyota Matrix. While driving approximately 65 MPH on normal road conditions, the contact downshifted to fourth gear and heard a grinding and squealing noise. The noise occurred without warning. The vehicle was taken to an independent mechanic for diagnostic testing and it was discovered that the gear bearings were worn, which resulted in gear fluid leakage from the seals. The gear fluid was dispensed into the fluid reservoir. The technician recommended replacing the manual transmission and clutch. The vehicle is currently inoperative and has not been repaired. The VIN was unknown. The failure and current mileages were 94,620.
2004 manual Toyota Matrix xr 1. I was hearing a very slight tinkling sound when at low rpms in 2nd, 3rd and 5th gears. When the clutch was pressed the sound went away. The sound was occurring for about 2 weeks before the failure. 2. Complete failure of the transmission. Driving in 5th gear and there was a whirring sound, a clunk, and the car jumped out of gear. Could not get into 1st, 2nd, 5th, or reverse. When car is neutral it is still in gear. We had significant trouble towing the car as I had to be inside the car with the clutch down as the tow truck driver pushed it. 3. Replacement of transmission.
Transmission complaints in other Matrix years
Frequently asked questions
How common are transmission problems on the 2004 Toyota Matrix?
NHTSA has 37 complaints about the transmission & drivetrain of the 2004 Toyota Matrix, 27% of the model year's 138 complaints. The component named most often is manual transmission (27 mentions).
Is there a recall for 2004 Toyota Matrix transmission problems?
No. NHTSA lists no transmission & drivetrain recall for the 2004 Toyota Matrix, though it has 1 recall for other components. If the problem is widespread, a repair may still be covered by an extended warranty or a manufacturer service bulletin — ask a dealer.
At what mileage do 2004 Toyota Matrix transmission problems start?
Half of the complaints with a recorded mileage happened before about 92,000 miles, and 14% before 25,000 miles.
Source: U.S. National Highway Traffic Safety Administration (NHTSA) — owner complaints through October 20, 2026, recalls and defect investigations; fuel economy from the EPA. Complaints are unverified reports and are not proof of a defect. How we rate model years.