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Clear aligners sit in your mouth for up to 22 hours a day. Over that time, bacteria, saliva proteins and food residue accumulate on the surface of the trays. Without regular cleaning, aligners develop an unpleasant smell, become visibly cloudy, and become a source of bacteria that is reintroduced to your mouth every time you put them back in.
The good news is that keeping aligners clean is straightforward. Here is exactly how to do it, what works, and what to avoid.
Why Cleaning Your Aligners Matters
Most people focus on keeping their teeth clean during aligner treatment. That is important, but the aligners themselves need equal attention. Here is why:
- Bacteria accumulation: the same bacteria that cause tooth decay and gum disease accumulate on aligner surfaces and are held in direct contact with your teeth for hours at a time
- Odour: uncleaned aligners develop a persistent smell within days. Volatile sulphur compounds produced by bacteria are the same compounds responsible for bad breath
- Discolouration: food, drink and bacterial buildup cause the transparent material to cloud and yellow, making the aligners visible in ways that defeat the purpose of wearing them
- Material degradation: bacterial and mineral buildup accelerates the breakdown of the thermoplastic material, which can affect fit over time
Daily Cleaning Routine
The most important habit is cleaning your aligners every time you remove them, before the saliva on them has a chance to dry.
Step 1: Rinse Immediately
As soon as you take your aligners out, rinse them under cool running water. This removes the majority of overnight or daytime saliva and surface bacteria before they dry and harden onto the tray. Always use cool water. Hot water warps the thermoplastic material and will affect the fit of your aligners.
Step 2: Brush Gently
Using a soft-bristled toothbrush, brush the inside and outside surfaces of your aligners with a small amount of mild liquid soap. Dish soap or hand soap both work well. Use gentle circular motions and work across all surfaces including the grooves where your teeth sit. Do not use toothpaste as most formulas contain abrasives that scratch clear aligner material, creating microscopic grooves where bacteria accumulate more easily and where clouding begins.
Step 3: Rinse Thoroughly
Rinse the aligners well under cool water until all soap residue is gone. Hold them up to the light to check for any cloudy patches or residue that needs more attention. Allow them to air dry briefly before reinserting or placing in the case.
Step 4: Clean Your Teeth Before Reinserting
Always brush and floss your teeth before putting your aligners back in after eating. Trapping food particles or residue against the teeth under a snug aligner tray significantly increases the risk of decay during treatment.
Deep Cleaning Once a Week
Daily brushing keeps surface bacteria in check, but a weekly soak removes mineral deposits and any buildup that regular brushing misses.
Option 1: Aligner or Retainer Cleaning Tablets
Cleaning tablets designed for aligners, retainers or dentures are the easiest and most effective deep clean option. Drop a tablet into a glass of cool water, place your aligners in the solution and leave for the time specified on the packet, typically 15 to 30 minutes. Rinse thoroughly afterward. These are inexpensive and widely available at pharmacies.
Option 2: White Vinegar Soak
Mix equal parts white vinegar and cool water. Soak your aligners for 20 to 30 minutes. The acetic acid kills odour-causing bacteria and dissolves calcium deposits that build up from saliva. Brush gently after soaking and rinse well. The vinegar smell disappears completely after rinsing.
Option 3: Baking Soda
Mix a small amount of baking soda with water to form a paste. Apply to the aligners with a soft brush, leave for a couple of minutes, then rinse thoroughly. Baking soda is mildly alkaline and helps neutralise the acidic bacterial environment that builds up on aligner surfaces. It also helps with minor discolouration.
What to Avoid
Some cleaning approaches that seem reasonable will actually damage your aligners.
- Toothpaste: abrasive particles in most toothpastes scratch clear aligner material, causing it to cloud faster and providing grooves for bacteria to accumulate
- Hot water: warps the thermoplastic material and affects the fit of your aligners
- Mouthwash: most mouthwashes contain alcohol which degrades clear plastic over time, causing discolouration and making the material more brittle
- Scented soaps: some heavily scented soaps leave a taste residue on the aligners. Use plain, unscented mild soap where possible
- Harsh chemicals or bleach: damages the material and leaves residue that is harmful to oral tissue
- Leaving them wet in a sealed case: traps moisture and creates ideal conditions for bacterial and mould growth. Allow aligners to air dry briefly before storing
How to Store Your Aligners
When your aligners are not in your mouth, they should be in their case. Every time. Not in a tissue, not on the bathroom counter, not in your pocket. In the case.
The case should be clean and ventilated. Rinse it with cool water and mild soap at least once a week. Allow it to dry fully before closing a clean aligner inside. A dirty case recontaminates freshly cleaned aligners immediately.
Keep your case and aligners away from direct sunlight, heat sources, and pets. Dogs in particular are attracted to the smell of dental appliances and will destroy them given the opportunity.
When you move to a new aligner set, do not throw the previous set away immediately. Keep it for a week or two in case you have a tracking issue and need to go back. Once your clinical team confirms the new set is tracking correctly, the old set can be discarded.
Frequently Asked Questions
Can I use toothpaste to clean my aligners?
No. Most toothpastes contain mild abrasives that are designed for enamel but will scratch clear aligner material. The scratches cause the material to cloud faster and create grooves where bacteria accumulate. Use mild liquid soap instead.
Can I soak my aligners in mouthwash?
Avoid it. Most mouthwashes contain alcohol which degrades clear plastic over time, causing discolouration and brittleness. Retainer or aligner cleaning tablets dissolved in cool water are a much better soaking option.
How often should I deep clean my aligners?
Once a week is sufficient alongside a daily rinse and brush routine. If you notice odour or discolouration developing between weekly deep cleans, increase the frequency or try a white vinegar soak.
My aligners have turned yellow. What do I do?
Yellowing is usually caused by bacterial buildup, food or drink exposure with aligners in, or using products like mouthwash that degrade the material. Try a soak in a 50/50 white vinegar and cool water solution for 30 minutes followed by gentle brushing. Significant yellowing from repeated coffee or tea exposure may be permanent, in which case completing that set and being more careful with the next one is the practical approach.
Can I put my aligners in the dishwasher?
No. Dishwashers use hot water and harsh detergents that will warp and damage your aligners. Always clean by hand with cool water and mild soap.
Should I clean my aligners in the morning or at night?
Both. Clean them every time you remove them. The most important clean is first thing in the morning after overnight wear, when the most bacterial buildup has accumulated. But a quick rinse and brush after every removal keeps odour and buildup from developing throughout the day.
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