There's no official, agreed cleaning protocol for clear aligners and retainers. But a handful of clinical studies have compared common methods head to head, and they point the same way: rinsing alone doesn't do the job, and a gentle brush plus a soak does better than either on its own.
Why aligners need more than a rinse
Aligners and retainers sit over your teeth for most of the day, and bacteria settle on them just as they do on enamel. Lab work has found that early bacterial attachment and biofilm growth on aligner plastics is similar to that on tooth enamel and metal braces [1]. Worn aligners also develop tiny scratches and grooves where plaque can collect [1].
There's also no natural help. Your tongue and cheeks normally help scrub your teeth, but they can't reach the inside of an aligner. That job is yours.
What the studies compared
- Water vs brushing. In a six-week study of 20 Invisalign patients, aligners only rinsed with water carried roughly three times the bacterial load of aligners brushed with toothpaste (583 vs 189 relative light units) [2].
- Brushing plus a soak. In that same study, brushing combined with an effervescent cleaning tablet gave the lowest bacterial readings of all three methods [1][2].
- Nine methods side by side. A small study tested nine strategies on aligners worn by five patients. Rinsing with water alone was the least effective; ultrasonic cleaning in a mild disinfecting detergent was the most effective [3]. A later review noted the ultrasonic bath also showed signs of damaging the plastic surface [1].
- Retainers too. In 21 people wearing clear retainers, brushing alone left more bacteria than brushing plus a peroxide-based tablet or brushing plus vinegar. The authors concluded brushing on its own isn't enough to keep retainers hygienic [4].
A 2022 systematic review pulled the aligner studies together. Its conclusion: combining a mechanical method (brushing) with a chemical one (a cleaning solution) looks most effective, but the studies are small and none can name a single best product [1].
Where to focus the brush
The same review found plaque builds up most on the inner surface behind the back teeth and along the biting edges of the front teeth [1]. These are the spots people tend to skip. Brush the inside of the aligner, not just the outside, and pay extra attention to those areas.
Watch what you brush with
A 2025 randomised trial looked at how five cleaners affected aligner colour and surface over two weeks of wear [5]:
- Plain, colourant-free clear soap had the smallest overall effect on colour and surface, and the authors called it a safe, inexpensive option for daily care.
- Cleaning crystals and whitening toothpaste caused the most.
- A denture-cleansing tablet left aligners looking clearest but visibly damaged the surface, so the authors advised against frequent use.
Every group showed some noticeable colour change after two weeks, so a little clouding is normal. What you use can make it better or worse.
A routine the evidence supports
- Rinse your aligners or retainer every time you take them out.
- Brush gently, inside and out, with a soft brush and a mild, clear, colourant-free soap. Avoid whitening toothpaste.
- Add a regular soak in an appliance cleaning solution. Follow the product's instructions and your orthodontist's advice.
- Brush your own teeth before putting aligners back in.
- Store them in a clean, dry case.
Our Retainer Cleaning Brush was designed to reach the inner grooves of aligners and retainers that a regular toothbrush struggles with. Whatever you use, the research is clear that the brushing step matters.
For the day-to-day routine broken down by retainer type, see How to Clean Retainers (Wire and Clear). For the cost and allergy comparison between tablets and a liquid cleaner, see Retainer Cleaner Tablets vs Liquid.
This article is general information, not medical advice. Always follow the cleaning instructions from your orthodontist or aligner provider.
References
- Charavet C, Gourdain Z, Graveline L, Lupi L. Cleaning and disinfection protocols for clear orthodontic aligners: a systematic review. Healthcare. 2022;10(2):340.
- Levrini L, et al. ATP bioluminometers analysis on the surfaces of removable orthodontic aligners after the use of different cleaning methods. Int J Dent. 2016;2016:5926941.
- Lombardo L, et al. Comparative SEM analysis of nine F22 aligner cleaning strategies. Prog Orthod. 2017;18:26.
- Sesli Çetin E, Şenişik NE, Akgün FA. Evaluation of the efficacy of different cleaning methods for orthodontic thermoplastic retainers in terms of bacterial colonization. Turk J Orthod. 2019.
- Kılıç B, Canpolat Ş, Öztürk M. Effect of different cleaning agents on colour and surface roughness of Invisalign clear aligners: a cross-over randomized controlled trial. BMC Oral Health. 2025;25:1745.