Clearing Sunroof Drains on 2008-2012 Toyota Highlander

Here’s a quick fix for the super-annoying problem of the Highlander’s sunroof drains clogging and flooding your footwells!

This assumes that you have already done your best to clear the drains from the sunroof drains itself. there are lots of videos and posts online on how to approach this. What I did was just open the sunroof and fish a long and thin wire cable through each drain hole. They are located in the front corners of the sunroof, about the diameter of a pencil. The rear drainage holes aren’t really accessible from the sunroof, but can be cleared from underneath the car just behind the wheel wells (you’ll need to remove the plastic covering to access the drain tubes).

Here’s a few pics of how I cleared the main drain location. You’ll need to pull back the carpeting and cable housings to get better access. I used a combination of vigorously poking a thin cable through the bolt holes and also using a large syringe with flexible tubing to flush it out. Eventually I was able to get the main drain cleared.

To clear the additional drains, what you want to do is get under the car and locate the exit holes. I used a thin bottle brush (like the kind used to clean those stainless steel straws). Just shove it in each hole and twirl it back and forth to clear the exit holes out. Hopefully, you will see a bunch of water come out if your drain is currently full of standing water.

There are 3 exit holes on each side. Here are the approximate locations. You are looking for an obvious little bump along the pinch welds:

Hopefully your problems will be solved once you have cleared the exit holes! Depending on how level your car is, you may not see water drain out of each hole.

Now, get out your wet-vac and suck up as much water as you can. Then remove the floor mats to help the floor dry out. I used a space heater on a low setting and checked on it throughout the day.

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  1. wow, genius! Thanks for posting the locations of the exit drains. Haven’t seen that posted anywhere else. Very helpful!

    1. I don’t think th body style changed until MY2014, so most likely they have the same drain locations as the 2012. Good luck!

  2. Holy smokes! The best description and pictures of the pain in the glass problem with the Highlander’s sunroof drainage system. Does anybody know where the end of the drain tube is located?

    1. I added a couple pics of where the front drains are located. The drain tubes are routed into a compartment by the footwell that is completely closed off and inaccessible, outside of some bolt holes. The rear sunroof drain tubes exit behind the rear wheels. Just remove the plastic shroud behind the rear wheels and you will see a tube poking out. You can then fish a long, thin/stiff cable up through it to try and clear them out.

    2. Yes, the front moon-roof drains Stop short of exiting the bottom of your car!
      The water drains out of the tube and is dumped Inside the door frame – mine has 1/2″ tubing (Big) and then the water is expected to exit/drain out of the pinch welds for the frame of the car.
      Clearing the pinch welds is a temporary fix on an older Highlander (mine, a 2008) as it is safe to assume that there is a Lot of debris and rust inside of the frame – on the bottom. The pinch welds will soon clog again.
      The drain hose must be extended to truly exit the bottom of the car.

    1. Mine, a 2008 as well. I found the end of the drain tubes. They do not exit the car!
      Carefully pull out the electrical junction box on the passenger side and reach in… you’ll find yours – short as well.

  3. Finally, something that worked to clear my drains!! I had tried everything and nearly given up.
    Thank you for your info and pictures.

  4. I am working on the passenger side drain on a 2013 MY. There is a straw sized tube (about the size of a fridge water supply) coming down from the drain and it runs along the entire right passenger rocker panel and disappears near the rear tire well. I have not been able to locate the end yet. Have you seen this setup on the Highlander? Was yours this way? The drivers side is the normal hose that just ends above the drain hole below it.

    1. Sounds like the rear sunroof drains. I did not know they ran along the rocker, but if you remove the plastic shroud behind the rear wheel, under the bumper, you will find the end of the tube.

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