Learn how to clean aligners properly with this step-by-step guide. Covers daily routines, deep cleaning, safe products, troubleshooting odour and stains, and what to avoid.
Knowing how to clean aligners properly is one of the simplest things you can do to keep your treatment on track — and your mouth feeling fresh. Yet it's surprisingly common for patients to develop habits that damage their trays, cause discolouration, or create unpleasant odours without realising what's going wrong. This guide gives you five practical, expert-backed tips for keeping your clear aligners clean, explains which products are safe (and which can cause real damage), and walks you through troubleshooting common issues like cloudiness, staining, and that telltale aligner smell.
📋 What This Guide Covers
- Quick answer: how to clean clear aligners
- Why aligners get cloudy or smelly (and what not to do)
- 5 expert tips: daily routine + weekly deep clean
- What products are safe — and which can damage aligners
- Troubleshooting: stains, odour, warping, white film
- Who clear aligners may not be suitable for
- Safety and compliance notes for UK patients
- FAQs
This guide is for anyone currently wearing clear aligners — whether you've just started treatment and want to build good habits from day one, or you've been wearing trays for a while and noticed they're not looking or smelling as fresh as they should. The same advice applies if you're wondering how to clean Invisalign or any other brand of removable aligner tray. If you also wear removable retainers after treatment, these tips work for those too — the same principles apply when you clean retainers.
Quick Answer: How to Clean Clear Aligners
Rinse your aligners under cool water every time you remove them. Brush them gently with a soft-bristled toothbrush and a small amount of clear, unscented liquid soap — not toothpaste, which is abrasive and can scratch the plastic. Once or twice a week, soak them for 15–20 minutes in a denture cleaner or aligner cleaning tablets dissolved in cool water. Never use hot water, mouthwash, or coloured soaps. Always brush your teeth before reinserting your trays.
Why Aligners Get Cloudy or Smelly — and What Not to Do
Before diving into the cleaning routine, it helps to understand what causes the problems in the first place. Clear aligners sit snugly against your teeth for 20–22 hours a day. During that time, several things happen:
- Bacteria accumulate: your mouth naturally contains bacteria. When a tray covers your teeth, saliva can't circulate as freely, and bacteria build up on both the tray and the tooth surfaces underneath
- Saliva dries and calcifies: saliva contains minerals. When it dries on the aligner surface, it can leave a chalky white film (calculus or tartar) that's difficult to remove once it hardens
- Food residue gets trapped: if you reinsert aligners without brushing your teeth first, food particles sit between the tray and your enamel — creating both odour and a decay risk
- Pigments stain the plastic: coffee, tea, red wine, turmeric, and other strongly coloured foods and drinks can discolour the plastic if consumed with trays in (or if residue is left on teeth when trays go back in)
Common Mistakes That Make Things Worse
- Using toothpaste to clean aligners: most toothpastes contain abrasive particles designed to clean enamel. On softer aligner plastic, these create micro-scratches that make the surface cloudy and give bacteria more places to hide
- Rinsing with hot water: clear aligner plastic can warp at temperatures above approximately 50–60°C. Hot water from the tap or kettle can permanently distort the tray, affecting its fit and effectiveness
- Using coloured or scented mouthwash: mouthwash can stain aligners (particularly green, blue, or purple varieties) and some formulas contain alcohol that may degrade the plastic over time
- Leaving trays out in the open air: when you're not wearing them, keep aligners in their case. Leaving them exposed allows bacteria to colonise the surface and the trays to dry out, making them harder to clean
5 Expert Tips: Daily Routine + Weekly Deep Clean
Here's a practical, step-by-step cleaning routine that keeps your aligners clear, fresh, and hygienic throughout your treatment:
Every single time you take your aligners out — for meals, snacks, or brushing — rinse them under cool running water. This washes away saliva and loose bacteria before they have a chance to dry on the surface. It takes five seconds and makes a significant difference. Don't use hot water — always cool or lukewarm.
At least twice a day — morning and evening — gently brush the inside and outside of each tray with a soft-bristled toothbrush and a small drop of clear, unscented liquid hand soap or washing-up liquid. This removes the bacterial biofilm that builds up during wear. Rinse thoroughly afterwards. Avoid toothpaste — the abrasives will scratch and cloud the plastic. Use a separate toothbrush from the one you use on your teeth.
Once or twice a week, give your aligners a deeper clean by soaking them in a cleaning solution. Drop an aligner cleaning tablet (or a denture cleaning tablet — they work on the same principle) into a cup of cool water, place your trays in, and soak for 15–20 minutes. Brush gently and rinse thoroughly afterwards. This helps dissolve mineral buildup and eliminate bacteria that daily brushing alone may miss. Some patients use aligner cleaning crystals — these are an alternative that works in a similar way.
This is arguably the most important hygiene habit during aligner treatment. After eating or drinking anything other than water, brush your teeth before putting the trays back in. If you can't brush, at the very least rinse your mouth vigorously with water. Reinserting aligners over teeth with food residue traps bacteria and sugars against your enamel — significantly increasing the risk of decay, bad breath, and tray discolouration.
Whenever your aligners are out of your mouth, they should be in their case — rinsed, clean, and stored properly. Don't wrap them in a napkin (they'll end up in the bin), don't leave them on a table or countertop (bacteria, pets, and accidents), and don't put them in your pocket loose (they can warp or crack). A clean case keeps them protected and hygienic until you reinsert.
Pro Tip: The Morning and Evening Routine
Build aligner cleaning into your existing brushing routine. Morning: remove trays → rinse trays → brush your teeth → brush the trays with soap → rinse → reinsert. Evening: same routine, plus this is a good time for a weekly deep soak while you eat dinner. Making it automatic means you won't forget — and your trays will stay clear and odour-free throughout treatment.
What Products Are Safe — and Which Can Damage Aligners
There's a lot of conflicting advice online about what you can and can't use to clean aligners. Here's a clear breakdown:
What About Bicarbonate of Soda or White Vinegar?
You'll find recommendations online for using bicarbonate of soda (baking soda) or white vinegar soaks. While these are less likely to cause immediate damage than toothpaste or hot water, they come with caveats:
- Bicarbonate of soda: mildly abrasive. A very dilute paste used occasionally is unlikely to cause significant scratching, but it's not as gentle as liquid soap and shouldn't be your daily go-to
- White vinegar soak: a 1:3 ratio of white vinegar to cool water for 15–20 minutes can help with mineral buildup. However, vinegar is acidic, and frequent or prolonged soaking may affect the plastic over time. Use sparingly — aligner cleaning tablets are a more purpose-designed option
Troubleshooting: Stains, Odour, Warping, and White Film
Even with a good routine, issues can crop up. Here's how to handle the most common ones:
😤 My Aligners Smell Bad
Cause: bacterial buildup, often from reinserting over unbrushed teeth or not cleaning trays frequently enough. Fix: soak in aligner cleaning tablets for 20 minutes, then brush gently with soap. Going forward, always brush your teeth before reinserting and rinse trays every time you remove them. If the odour persists despite good hygiene, mention it to your clinician — it could indicate an oral health issue that needs attention.
☁️ My Aligners Look Cloudy
Cause: usually micro-scratches from using toothpaste or a hard-bristled brush. Can also be caused by dried saliva mineral deposits. Fix: if it's mineral buildup, a deep soak in cleaning tablets or a brief dilute vinegar soak may help. If it's scratching, unfortunately the damage is permanent — switch to liquid soap for future trays. Cloudiness from scratching gets worse over time as bacteria settle into the grooves.
🟡 My Aligners Are Stained Yellow or Brown
Cause: drinking coffee, tea, or red wine with aligners in, or reinserting over teeth with pigment residue. Smoking also stains trays heavily. Fix: mild staining may respond to a cleaning tablet soak. Heavy staining is usually permanent. The best prevention is always removing trays before consuming anything other than plain water, and brushing your teeth before reinserting. Since you change trays every 1–2 weeks, the staining won't be permanent across your treatment.
⬜ There's a White Chalky Film on My Aligners
Cause: calcium and mineral deposits from saliva (essentially tartar forming on the tray rather than on your teeth). Fix: soak in a denture or aligner cleaning tablet solution, then brush gently. A brief dilute vinegar soak can also help dissolve mineral buildup. Prevent it by rinsing trays immediately when you remove them — don't let saliva dry on the surface.
🔥 My Aligner Has Warped or Doesn't Fit
Cause: exposure to heat — hot water, being left in a hot car, put in the dishwasher, or drinking hot beverages with the tray in. Fix: a warped tray cannot be fixed. Contact your clinician — they may advise moving to the next tray early or ordering a replacement. Do not try to reshape it yourself. Prevention: always use cool water, store in the case, and remove before hot drinks.
Who Clear Aligners May Not Be Suitable For
While this guide focuses on cleaning, it's worth noting that clear aligners aren't suitable for every patient. They may not be the right option if:
- Your case is clinically complex: severe crowding, significant bite correction, or cases requiring extractions may be better managed with fixed braces
- You have active gum disease or untreated decay: oral health must be stabilised before any orthodontic treatment begins
- Consistent wear isn't realistic: aligners need to be worn 20–22 hours per day. If this doesn't suit your lifestyle, fixed braces remove the compliance variable
- You struggle with the cleaning routine: if maintaining good oral hygiene and tray hygiene during treatment is genuinely difficult, your clinician can discuss alternatives that may be easier to manage
If you're considering treatment and want to understand which option suits your case, book a consultation to discuss your situation with a clinician.
🚩 Signs That Need Clinical Attention
- Persistent bad breath or aligner odour despite thorough cleaning
- Red, swollen, or bleeding gums
- White spots appearing on your teeth (early sign of decalcification)
- A warped tray that no longer fits properly
- Pain or sensitivity that doesn't resolve within a few days of a new tray
- Visible decay or new cavities during treatment
If you notice any of these, contact your treating clinician. Good hygiene prevents most issues, but early clinical intervention prevents small problems from becoming bigger ones.
Safety and Compliance Notes for UK Patients
A few important points for UK patients regarding aligner care and treatment oversight:
GDC Standards
The General Dental Council requires that all orthodontic treatment — including clear aligner therapy — is provided by, or under the supervision of, a GDC-registered dental professional. This includes guidance on oral hygiene and tray care during treatment. If your provider hasn't given you clear cleaning instructions, ask for them — it's part of the standard of care.
Direct-to-Consumer Aligner Services
The GDC has published specific guidance on aligners sent directly to your home. One concern with remote-only services is the lack of ongoing clinical monitoring — issues like decay developing under trays, gum problems, or poor tracking may not be identified early without regular check-ups. Proper cleaning reduces but doesn't eliminate these risks.
Oral Health During Treatment
Good aligner hygiene is important, but it's not a substitute for regular dental care. Continue attending routine dental check-ups and hygienist appointments during your treatment. Your clinician can spot early signs of issues — such as decalcification, gum recession, or decay — that you might not notice yourself. You can review what's included in our treatment packages to understand how monitoring is structured.
Frequently Asked Questions
How do you clean clear aligners properly?
Rinse them under cool water every time you remove them. Brush them gently twice a day with a soft-bristled toothbrush and clear, unscented liquid soap (not toothpaste). Once or twice a week, soak them in aligner cleaning tablets or denture cleaning tablets dissolved in cool water for 15–20 minutes. Always brush your teeth before reinserting the trays.
Can you use toothpaste on aligners?
No — most toothpastes contain abrasive particles that will scratch the surface of your aligner plastic. These scratches make the trays look cloudy and create microscopic grooves where bacteria can accumulate. Use clear liquid soap instead for daily cleaning.
How do you clean Invisalign trays specifically?
The same way you'd clean any clear aligner. Invisalign offers its own branded cleaning crystals, but denture cleaning tablets or aligner cleaning tablets from any reputable brand work on the same principle. The daily routine — rinse, brush with soap, and brush teeth before reinserting — applies to all clear aligner brands equally.
Why do my aligners smell bad?
Aligner odour is almost always caused by bacterial buildup. The most common culprits are: not rinsing trays when you remove them, reinserting over teeth that haven't been brushed, not cleaning trays regularly enough, or leaving trays out of the case where bacteria can colonise the surface. A deep soak in cleaning tablets and improved daily hygiene usually resolves it within a day or two.
Are aligner cleaning tablets necessary, or are they a gimmick?
They're not strictly essential — daily brushing with soap and rinsing is the foundation of good aligner hygiene. However, cleaning tablets do provide a deeper clean that helps dissolve mineral buildup and kill bacteria that brushing alone may miss. Using them once or twice a week is a worthwhile addition to your routine. Denture cleaning tablets are an affordable alternative to branded aligner-specific products.
Can I soak my aligners in mouthwash?
It's not recommended. Coloured mouthwash can stain your trays green, blue, or purple. Alcohol-based mouthwash may degrade the plastic over time. If you want an antimicrobial soak, aligner cleaning tablets are specifically designed for the purpose. Use mouthwash on your teeth and gums — not on the trays themselves.
How do I clean retainers after treatment?
If you wear removable retainers after your aligner treatment, the same cleaning principles apply. Rinse after removal, brush gently with clear soap, and soak weekly in cleaning tablets. Retainers are worn long-term, so good cleaning habits are even more important — a well-maintained retainer can last significantly longer before needing replacement.
What's the white chalky buildup on my aligners?
That's mineral deposits from your saliva — essentially tartar forming on the plastic rather than on your teeth. It happens when saliva dries on the tray surface. Prevent it by rinsing trays immediately when you remove them. Remove existing buildup with a cleaning tablet soak or a brief soak in a dilute solution of white vinegar and cool water (1:3 ratio), followed by gentle brushing.
How often should I replace my aligner case?
Replace your aligner case every few months, or sooner if it becomes discoloured, develops an odour, or shows visible buildup. Wash the case regularly with soap and water and allow it to air dry. A dirty case recontaminates clean aligners — there's no point cleaning your trays meticulously if you're putting them back into a bacteria-laden case.
📚 References and Further Reading
- NHS — Orthodontics Overview
- NHS — How to Keep Your Teeth Clean
- GDC — Aligners or Braces Sent Directly to Your Home
- GDC — Guidance on Advertising
- British Orthodontic Society — Patient Information: Retainers (PDF)
- British Orthodontic Society — Patient Information and Resources
- British Dental Association — Teeth and Gum Care
Considering Clear Aligners?
Book a no-obligation consultation. We'll assess your case, explain the full treatment process — including care and cleaning — and answer all your questions honestly and without pressure.
Book Your ConsultationDisclaimer: This article is for general information only and does not constitute dental or medical advice. Every case is different, and treatment suitability can only be determined through an in-person clinical assessment by a GDC-registered dental professional. Product recommendations are general guidance — always follow the specific cleaning instructions provided by your treating clinician.
Written by Pro Aligners Team
Medically reviewed by Pro Aligners Team • GDC: 195843