Cleaning Invisalign Trays: A Daily and Weekly Routine
The simplest way to clean Invisalign trays is a short daily routine. Rinse them in lukewarm water, brush them gently with a soft toothbrush and clear soap, and soak them once a week. Never use hot water. Keep trays away from harsh products like denture cleaners and bleach. Below we explain each step, what to skip, and how to keep the teeth under your aligners clean too.
We are Mersaldental, a family dental office in downtown Ottawa. We accept new patients, bill insurance directly, and accept CDCP. If a tray cracks, smells no matter what you do, or your gums are sore, visit our site to book. We also see dental emergencies.
TL;DR
Every day: rinse your trays when you take them out, then brush them gently morning and night with a soft toothbrush and clear, unscented soap.
Once a week: soak your trays for 15 minutes in a cleaning solution made for aligners, then rinse for at least 30 seconds.
Never use hot or boiling water, denture cleaners, bleach, or colored or alcohol-based mouthwash. They can warp, dull or stain the plastic.
Clean your teeth before every reinsertion. Interdental brushes usually beat floss for gum health, but the best tool is the one you will actually use.
Cloudy, cracked or smelly trays that do not improve are a reason to call your dentist, not to try stronger products.
Table of Contents
Why clean aligners matter more than you might think
Your aligners sit against your teeth and gums for most of the day, and for 20 to 22 hours of it you are eating nothing and drinking only water. Saliva, bacteria and food particles get trapped between the plastic and your teeth. If the tray is not clean, you are holding that film against your enamel and gums.
The usual signs of a neglected tray are easy to spot:
A cloudy or dull look
A sour or musty smell
A bitter taste when you put them in
White or yellowish film on the plastic
The aligners are meant to be replaced every couple of weeks, but they still need to be cleaned the whole time. Otherwise they can smell and look bad quickly.
That white gunk many patients ask about is usually plaque and mineral buildup from saliva and water. It is not a sign that something is wrong with your treatment. It is a sign that your trays need a gentler, more regular routine.
The daily routine: about 30 seconds, twice a day
This is the part that matters most. Doing it consistently works better than any product you buy.
Rinse when you remove them. Any time the trays come out, rinse them under lukewarm water. This stops saliva from drying onto the plastic, which is what makes film harden.
Brush gently. Use a soft-bristled toothbrush, ideally one you keep only for your aligners. Brush the inside and outside, including the grooves where your molars sit.
Use clear, unscented soap. A small drop of clear liquid hand soap in lukewarm water is gentle and effective. Official guidance from Invisalign Canada also lists a soft-bristled toothbrush, mild toothpaste and lukewarm water as a way to clean aligners. We prefer soap, because many toothpastes contain abrasives that can leave tiny scratches in clear plastic. Scratches collect stains and make trays look cloudy.
Rinse again. Rinse until you see no soap, then put the trays back in or into their case.
Brush your teeth before the trays go back in. Otherwise you are sealing food and bacteria against your enamel.
Always use lukewarm water
Heat is the one thing that can ruin a tray in seconds. Hot or boiling water can warp the plastic, and a distorted aligner no longer matches the movement your dentist planned. Stick to lukewarm or tepid water. If you can feel the heat on your wrist, it is too hot. The same goes for the dishwasher, a hot car dashboard and the microwave.
The weekly soak
Daily brushing keeps most trays clear. A weekly soak lifts what brushing misses and helps prevent that cloudy look.
The most direct option is a product designed for the job. According to Invisalign Canada, Invisalign Cleaning Crystals work with a 15-minute soak: dissolve one packet in a cleaning tub of warm water, add the aligners, then rinse. Follow the label’s temperature advice, and keep it lukewarm.
How to do it well
Pick a fixed day. Treating the soak as an anchored weekly routine, like Sunday meal prep, makes people far more likely to actually do it than treating it as something to do when the trays look bad.
Rinse for at least 30 seconds afterward. Residue from crystals or tablets tastes bitter and can irritate your gums when the tray goes back in.
Consider filtered water if your water is hard. One orthodontic practice notes that hard tap water can work against cleaning agents. If you live where kettles scale up quickly, filtered or bottled water for the soak may keep trays clearer.
Brush after soaking. A soak loosens buildup, and a soft brush finishes the job.
Cleaning crystals alternatives
Many patients ask what they can use if they do not want to buy crystals. Here is how the common options compare.
Method | How it works | Our view |
Clear unscented soap and soft brush | Daily brushing in lukewarm water | Best everyday method. Cheap and gentle. |
Cleaning crystals | 15-minute weekly soak | Good for weekly refresh and for retainers. |
UV sanitizing case | Uses UV-C light, no water | Convenient for travel. Not a replacement for brushing. |
Diluted white vinegar | Short soak, then brush and rinse | Occasional use only if there is heavy buildup, and only after checking with us. |
Denture tablets | Strong cleaners | Avoid. They are not made for aligner plastic. |
On the UV option: the Invisalign UV Sanitizing Case is described as using UV-C light to treat the trays in 5 minutes, with no water or chemicals. It is a handy extra when you are travelling. A light does not remove film, so keep brushing.
What not to use
Most damage to aligners comes from well-meant cleaning with the wrong thing. Skip these:
Hot or boiling water. It can warp the trays, as above.
Denture cleaners and bleach. Guidance for aligner care advises against them because they can dull the plastic, discolor it or leave residue that irritates your mouth.
Colored or scented mouthwash. Alcohol-based rinses in particular can dry out and damage the trays, according to the same guidance. Colored ones can stain.
Abrasive toothpaste. Whitening pastes with gritty particles scratch clear plastic.
Wrapping trays in a napkin. This is how many trays end up in the garbage. Use the case every time.
Cleaning choice matters for appearance too. A 2026 laboratory study on clear aligner materials found that clarity and color stability depend on both the material and the cleaning protocol, and that Invisalign aligners held their color better than some other tested brands. That was an in vitro study, not a study of patients, but it supports the idea that gentle, consistent cleaning protects how your trays look.
Cleaning your teeth: interdental brushes or floss?
A clean tray on dirty teeth does little good. Patients often ask whether interdental brushes or floss is better, so here is the short version.
An evidence review from the Oral Health Foundation reports that interdental brushes tend to improve gum health slightly more than floss in the short term. The benefit appears greater in people with gum disease or open spaces between teeth. The same review says the advantage is modest and the certainty of the evidence is often low. Technique and regular use matter a lot.
In practice:
Tight contacts, no visible gaps: floss or floss picks are usually the right tool.
Visible gaps, gum recession or bleeding gums: an interdental brush often reaches more surface. Your hygienist can tell you which size to use, since a brush that is too big hurts and one that is too small does nothing.
Attachments and wider spaces: if you have small bumps bonded to your teeth, you may find a brush easier than floss. Our guide to Invisalign attachments explains what they are and how to look after them.
After IPR: if your dentist has made small spaces between teeth, ask which tool suits those areas. We cover that in our article on IPR with Invisalign.
Either tool beats skipping it. Pick the one you will use daily, ideally before bed, before the trays go in for the night.
Cleaning after meals and when you are out
You will take your trays out to eat, so build a pattern around it.
Take out the trays and put them in their case. Never in a pocket or on a tray table.
Eat or drink.
Brush your teeth. If you cannot, rinse with water and brush at the first chance.
Rinse the trays and put them back.
Coffee, tea, red wine and colored drinks are the usual stain culprits, and sugary drinks left under a tray keep sugar against your teeth. Our guide on eating and drinking with Invisalign covers what is safe with trays in and what is not.
Whitening is another question patients raise during treatment. If you want a brighter smile, ask us before you try anything at home. There is a useful overview of whitening with Invisalign safely for Canadian patients, and we can advise on timing and on our own teeth whitening options once your aligners are finished.
Our perspective: what we see in the chair
We see patients at their check-ups with trays that are scratched, clouded or discolored, and nearly always the cause is the same. The patient was working hard but using the wrong product. Hot water, strong cleaners and abrasive toothpaste are the usual culprits.
Our advice is plain. Keep the routine short enough that you will do it every day. Brush gently, rinse well, use lukewarm water, and add a weekly soak. Spend the extra minute on your teeth, not on a stronger cleaner for the trays.
We also want you to feel comfortable calling us. A tray that cracks, a gum that bleeds for more than a few days, or a tooth that hurts under an aligner should not wait for your next appointment. We are a family office with a multilingual team, and we would rather answer a small question early than treat a bigger problem later.
— Mersal
When cleaning is not enough
Some problems are not about cleaning, and no product will fix them.
Cracked or split tray. Do not keep wearing it if the edge is sharp. Follow the steps in our guide to a cracked Invisalign tray and contact us.
Persistent odor or taste after cleaning. This can point to a gum or tooth problem under the tray, such as plaque buildup or a cavity. Book a check-up.
Swelling or extreme redness in the mouth. Aligner plastic can rarely cause an allergic reaction. One manufacturer’s instructions for a clear aligner system advise patients to stop use and see a health care professional if swelling or extreme redness occurs. Remove the tray and call us or your doctor.
Sore teeth and gums in the first week. Some soreness is common with new trays. See our first-week pain plan.
Wear schedule questions. Some complex cases may call for a slower tray change, such as 14 days instead of weekly. A review of aligner evidence notes that the evidence for a one-week change is lacking for many movements. Always follow the schedule your own dentist gives you.
Once treatment ends, you will likely wear retainers, and they need the same gentle care. See retainers after Invisalign for what to expect.
Invisalign and dental care at Mersaldental
If you are thinking about aligners, or you are already wearing them and want a professional check, we can help. We offer Invisalign in downtown Ottawa, along with professional cleanings, which remove buildup that home care cannot. We bill insurance directly and accept CDCP and IFHP. You can read about our Invisalign consultations and how long treatment usually takes.
We also offer same-day treatment and emergency care, so if something goes wrong with a tooth or a tray, you do not have to wait.
A simple weekly checklist
Print this or save it on your phone.
When | What to do |
Every time you remove trays | Rinse with lukewarm water, store in the case |
Morning and night | Brush trays gently with soft brush and clear soap |
Before reinserting | Brush teeth and clean between them |
Once a week | 15-minute soak, then rinse for 30 seconds or more, then brush |
At each check-up | Show us your trays and ask about any stains or smells |
FAQ
What should I use to clean my Invisalign tray?
Use a soft toothbrush with clear, unscented soap and lukewarm water every day. Once a week, soak the trays in a cleaning solution made for aligners. Avoid hot water, denture cleaners, bleach and colored or alcohol-based mouthwash.
What is the white gunk on my Invisalign trays?
It is usually plaque and mineral deposits from saliva and water. Brushing daily and soaking weekly usually keeps it from building up. If it keeps coming back or the tray smells even when clean, we can check your teeth and gums.
Can I use toothpaste on my aligners?
A mild toothpaste is listed in Invisalign Canada’s guidance as an option. We suggest clear soap instead, because gritty or whitening toothpastes can scratch the plastic. If you use toothpaste, choose a mild, non-abrasive one.
Are interdental brushes better than floss with Invisalign?
Often, but not always. Brushes tend to do slightly better for gum health, especially where there are gaps or gum disease, while floss suits tight contacts. Ask your hygienist to size the brush for you.
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