How to Clean Your Aligners the Right Way?

Whether you're just beginning your clear aligner journey or have been wearing them for months, properly cleaning your aligners is key to maintaining oral health, preserving their appearance, and ensuring the overall success of your treatment.

Aligners are practically invisible to others, but they are not self-cleaning. Food particles, plaque, and bacteria can easily build up unless proper aligner hygiene is followed. Failing to sanitize your aligners can quickly result in bad breath, cloudy or discolored trays, and even serious oral health issues like cavities and gum irritation.

This comprehensive guide will take you through everything you need to know, from routine cleaning to deep sanitation, to keep your aligners clean and your smile shining.

Why Cleaning Your Aligners Matters?

Let’s keep it simple. Why is cleaning your aligners important?

Since you wear them for 20 to 22 hours every day, they’re constantly exposed to your saliva, leftover food, and natural mouth bacteria. If you don’t clean them properly, that bacteria can quickly build up and cause:

• Bad breath
• Visible discoloration
• Tartar buildup
• Mouth irritation or sores
• Less effective treatment as the trays get cloudy or damaged

By learning how often to clean aligners and following a consistent routine, you prevent unwanted complications and keep your trays nearly invisible, exactly as they should be.

How Often Should You Clean Aligners?

People often wonder how frequently they should clean their aligners. The simple answer: clean them every time you take them out, and also in the morning and at night.

Here’s a quick guide:

• Daily: Rinse and brush your aligners gently twice a day, once in the morning and once at night.
• Every Time You Remove Them: Rinse with lukewarm water to wash away saliva and avoid buildup.
• Weekly: Deep clean them with special cleaning tablets or crystals to sanitize and remove odors.

How to Clean Aligners Daily?

You don’t need a complicated process to keep your aligners clean. Just follow these easy steps:

Rinse Right after Taking Them Out

Use lukewarm water (never hot) to rinse your aligners. This keeps saliva from drying on them and creating bacteria.

Brush Gently with a Soft Toothbrush

Use a separate, soft-bristle toothbrush, not your regular one. Avoid using toothpaste; it can scratch the surface and make your aligners look cloudy.

Use Clear, Unscented Antibacterial Soap (Optional)

A few drops of gentle soap can help remove bacteria and oils. Just rinse them well before putting them back in your mouth.

How to Remove Stains from Aligners?

Stains can make even the best aligners look dirty. If your trays are starting to look yellow or foggy, don’t panic. Here’s how to clean aligners and restore their clarity:

Use Cleaning Tablets (H3)

Specialized aligner cleaning solutions, such as clear aligner cleaning crystals or retainer cleaning tablets, are excellent for removing stubborn stains.

• Drop a cleaning tablet (like a denture cleaner or clear aligner cleaning crystal) into a cup or bowl of warm water. Make sure the water isn’t too hot.
• Put your stained aligners into the water and ensure they’re fully covered.
• Let them soak for about 15–20 minutes.
• After that, rinse them well under running water before putting them back in your mouth.

Hydrogen Peroxide Mix

You can also use a mix of hydrogen peroxide and water to clean tough stains:

• Mix equal parts hydrogen peroxide (readily available at any pharmacy) and lukewarm water in a clean container large enough to fully submerge your aligners.
• Soak your aligners in this solution for about 30 minutes.
• Take them out and rinse them well with water.
• Brush your teeth before putting the aligners back in.

These methods work well for removing stains, but they’re not a substitute for regular cleaning and good oral hygiene. Ensure you still brush and floss your teeth, and clean your aligners daily using a gentle cleaner or clear antibacterial soap.

Also, avoid drinking colored drinks (such as soda, coffee, or juice) while wearing your aligners. After eating or drinking anything other than water, rinse your aligners with plain water to keep them clean and clear.

Baking Soda Paste

Mix baking soda with water to form a paste. Gently brush stained spots, then rinse well.

How to Deep Clean Aligners Weekly?

Keeping your clear aligners clean every day helps stop stains and bacteria from building up. However, giving your aligners a deeper clean once a week is a smart habit to ensure they remain clear, fresh, and continue working effectively.

Here are two ways to do that:

Soaking in Denture Cleaner

An easy way to deep clean your aligners is by soaking them. Simply drop a denture cleaning tablet into a cup of lukewarm water and soak your aligners for the recommended time listed on the product packaging. After soaking, rinse them well with water before putting them back in your mouth. This helps away tough stains and germs that may have built up during the week.

Using an Ultrasonic Cleaner

Another effective option is an ultrasonic cleaner, which uses high-frequency sound waves to gently dislodge dirt, plaque, and buildup from hard-to-reach areas on your aligners. Just place your trays into the machine with water or a cleaning liquid, and follow the directions that come with it. This method works great for cleaning out stubborn stains and bacteria.

Don’t forget, cleaning your aligners every day, along with a deep clean each week, helps them work better and keeps them looking good throughout your treatment.

What Not to Do When Cleaning Aligners?

Taking care of your aligners isn’t just about doing the right things; it’s also about avoiding the wrong ones. Certain common mistakes can damage your aligner trays, cause them to appear cloudy, or even interfere with their ability to straighten your teeth effectively.

Here are a few things you definitely shouldn’t do:

Don’t Use Hot Water

It might seem like hot water would clean better, but it can ruin your aligners. The plastic is sensitive to heat and can bend or change shape if the water is too hot. This can make them fit poorly and disrupt your treatment. Always rinse or soak them in cool or lukewarm water only.

Don’t Brush with Toothpaste

Toothpaste is made for teeth, which are much harder than aligners. Most kinds have little gritty particles that help clean teeth, but can scratch up your aligners. These tiny scratches can make your trays look cloudy and trap bacteria and stains. Instead, use a soft toothbrush with clear soap or a cleaner made specifically for aligners.

Aligner Hygiene Routine: Daily & Weekly Schedule

Daily

Morning: Take out aligners, brush your teeth and aligners, rinse everything well.

Midday: Take out before meals, rinse the trays, and store them in a clean case.

Evening: Brush and floss your teeth, clean aligners again, and rinse thoroughly before bedtime.

Weekly

• Choose a day to deep clean
• Soak aligners or use an ultrasonic cleaner
• Check for cracks or wear
• Replace your aligner cleaning toothbrush every 4–6 weeks

Aligners and Oral Hygiene: Keeping Your Mouth Clean Too

Your trays aren’t the only thing that needs attention. Poor oral hygiene can negatively impact the appearance, smell, and effectiveness of your aligners, leading to discoloration, bad breath, and reduced treatment results.

• Clean aligners won’t help much if your mouth isn’t clean
• Brush your teeth after every meal before putting trays back in
• Floss daily to keep food from getting stuck under the aligners
• Use alcohol-free mouthwash for fresh breath and fewer germs

Traveling with Aligners: Keeping Them Clean On-the-Go

Even when traveling, you can keep up your routine. Pack a travel kit with:

• A toothbrush
• Clear soap
• Cleaning tablets
• A portable aligner case
• Disposable floss picks

Stay consistent, even on the go!

When to Replace or Contact Your Provider

Sometimes cleaning isn’t enough. Call your dentist or orthodontist if you notice:

• Cracks or holes
• Cloudiness that won’t go away
• A warped shape
• A strong odor that doesn’t go away after cleaning
• Getting a replacement quickly keeps your treatment on track

Introducing ALIGNERCO Aligner Cleaner + Whitener

Keep your aligners clean, fresh, and shiny with our Aligner Cleaner + Whitener foam. This special product not only keeps your aligners clear but also helps whiten your teeth, so your smile stays bright and healthy throughout your treatment.

Key Features

Cleans and Whitens at the Same Time

This 2-in-1 foam keeps your aligners clean while gently whitening your teeth.

Works on Different Devices

Perfect for cleaning not just aligners, but also works well with retainers, mouth guards, and whitening trays.

Made with Safe Ingredients

It contains gentle but effective ingredients like Hydrogen Peroxide, Xylitol, and Menthol.

Removes Buildup

The formula is made to deep clean, getting rid of plaque, bacteria, and stains that collect during daily wear.

Whitening Boost

It helps brighten your smile by whitening your teeth while you wear your trays.

Super Easy to Use

No brushing or soaking needed. Just pump some foam into the tray, spread it out, wear your aligners, and spit out any extra foam.

How to Use?

Here’s a simple step-by-step guide to using the ALIGNERCO Cleaner + Whitener.

Final Takeaways: Clean Aligners, Confident Smiles

Keeping your aligners clean is important, not just to keep them clear but also to protect your teeth and make sure your treatment goes smoothly. A good cleaning routine, avoiding mistakes like using hot water or toothpaste, and being consistent with daily and weekly cleanings will help you take care of both your trays and your smile. Clean aligners mean less bacteria, fewer stains, fresher breath, and a faster journey to the smile you’re aiming for.

To make cleaning even easier, try ALIGNERCO Aligner Cleaner + Whitener . This all-in-one cleaner helps remove buildup, freshen up your trays, and gently whiten your teeth. Just soak your aligners in it for a few minutes each day to keep them clear and odor-free. It’s safe, works well, and fits perfectly into your aligner care routine.

With ALIGNERCO, taking care of your aligners is simple, so you can stay focused on getting that perfect smile, one clean tray at a time.