After strep throat, your Invisalign aligners need a thorough disinfection, not just a routine rinse. The bacteria that cause strep can survive on dry surfaces for days to months, so any aligners you wore while sick are potentially contaminated. The good news: a proper soak with common household products can eliminate the bacteria, and your risk of reinfecting yourself through your aligners is actually quite low once you’ve started antibiotics.
Why Your Aligners Need Extra Cleaning
Group A Streptococcus, the bacterium behind strep throat, is surprisingly hardy on surfaces. Research from Boston University found it can survive on dry surfaces anywhere from 3 days to 6.5 months. Your aligners sit against your teeth and gums for 20+ hours a day, creating a warm, moist environment where bacteria thrive. While doctors generally agree that aligners aren’t a major source of reinfection, especially once antibiotics are working, a deep clean gives you peace of mind and eliminates any lingering bacteria from the plastic.
The Best Disinfection Methods
Hydrogen Peroxide Soak
This is the most accessible and effective option for killing strep bacteria at home. Mix equal parts hydrogen peroxide (the standard 3% concentration from any drugstore) and lukewarm water. Submerge your aligners completely and let them soak for 15 to 30 minutes, then rinse thoroughly under cool water before putting them back in your mouth. Hydrogen peroxide is a broad-spectrum disinfectant that breaks down into water and oxygen, so it won’t leave chemical residue on the plastic.
Chlorhexidine Rinse
If you have chlorhexidine mouthwash (0.12% concentration, sold under brand names like Peridex or Periogard), it’s a strong option. A clinical trial on removable orthodontic appliances found that spraying them with 0.12% chlorhexidine even once a week significantly reduced streptococcal colonies and biofilm on the plastic surfaces. You can spray or soak your aligners with this rinse for a few minutes, then rinse with water. One downside: chlorhexidine can cause slight staining on the plastic with repeated use, so it’s better suited as a one-time deep disinfection rather than a daily habit.
Denture Cleaning Tablets
Effervescent denture tablets (like Polident or Retainer Brite) dissolve in water and create an antimicrobial solution. Drop a tablet in a cup of lukewarm water, place your aligners in the fizzing solution, and soak for the time listed on the packaging, usually 15 to 20 minutes. These are convenient and widely recommended by orthodontists for routine cleaning, and they work well as part of a post-illness disinfection routine.
What About Invisalign Cleaning Crystals?
Invisalign’s official cleaning crystals contain sodium dichloroisocyanurate (a chlorine-releasing compound) along with surfactants that help break up buildup. They’re designed to freshen and clean aligners, but they aren’t marketed as antibacterial. If you already have them on hand, they’re fine as one step in the process, but pairing them with a hydrogen peroxide soak gives you stronger disinfection after an active infection like strep.
Don’t Forget the Storage Case
Disinfecting your aligners while ignoring the case defeats the purpose. Your case has been holding contaminated aligners for days, and bacteria can linger in the corners and crevices of the plastic.
Wash the case thoroughly with mild dish soap and a soft-bristled toothbrush, scrubbing the interior corners where grime collects. For deeper disinfection, soak it for about 15 minutes in a solution of warm water mixed with white vinegar or a few drops of antibacterial dish soap. You can also drop a denture cleaning tablet in with it. The most important step afterward: dry the case completely before putting your aligners back in. Moisture promotes bacterial growth, so let it air dry fully in a well-ventilated spot or pat it dry with a clean towel.
Avoid bleach or abrasive cleaners on the case. They can damage the plastic and leave residue that transfers to your aligners.
Timing: When to Clean and When to Toss
If you’re still on your current set of aligners and have several days left before switching, disinfect them right away using the hydrogen peroxide method. If you’re within a day or two of switching to your next tray, you can simply move to the fresh set and disinfect the old ones before storing them (in case you ever need to go back to a previous tray).
You generally don’t need to throw away aligners after strep. Once antibiotics have been active in your system for about 24 hours, you’re typically no longer contagious, and a properly disinfected aligner won’t harbor enough bacteria to reinfect you. Multiple orthodontists confirm there’s no contraindication to continuing your aligner treatment through a course of antibiotics, as long as you’re keeping the trays clean.
Preventing Buildup While You’re Sick
When you’re actively fighting strep, your mouth produces more bacteria than usual, and you may be mouth-breathing more if your throat is swollen, which dries out both your mouth and your aligners. A few habits help during this window:
- Rinse aligners every time you remove them. Even a quick rinse under cool water prevents saliva and bacteria from drying onto the surface.
- Brush aligners gently with a soft toothbrush. A light scrub with a separate soft-bristled brush (not the one you use on your teeth) removes the film that builds up faster during illness.
- Stay hydrated. Drinking water throughout the day flushes bacteria from around the aligners and keeps your mouth from becoming a more hospitable environment for bacterial growth.
- Avoid hot water on the trays. It’s tempting to use warm or hot water for cleaning when you’re focused on killing germs, but water above about 150°F can warp the thermoplastic and ruin the fit of your aligners.
Once your antibiotic course is finished and you’re feeling better, do one final deep clean of both your current aligners and your case. That marks a clean slate, and you can go back to your normal cleaning routine from there.