How to Use the Invisalign Aligner Cleaning System Correctly
The Invisalign aligner cleaning system is designed to keep your aligners fresh, clear, and odor-free throughout treatment. While many patients think rinsing with water is enough, proper cleaning requires more than that. This guide explains exactly how to use the system, explores alternative cleaning options, and helps you choose the best routine for healthy, clear aligners.
Why Cleaning Aligners Matters
Clear aligners are worn up to 22 hours per day, making them prone to:
-
Odor if not cleaned properly.
-
Cloudiness that reduces the “invisible” look.
Neglecting daily aligner cleaning not only affects appearance but also impacts oral health.
What Comes in the Invisalign Aligner Cleaning System?
The official system typically includes:
-
Cleaning tub – a small container for soaking aligners.
-
Invisalign cleaning crystals – the branded cleaning solution.
-
Instructions – step-by-step usage details.
These crystals are marketed as the safest way to clean aligners without scratching or discoloring them.
Step-by-Step: How to Use Invisalign Cleaning Crystals
Step 1: Prepare Your Cleaning Tub
Fill the tub with lukewarm water (never hot, as it can warp your aligners).
Step 2: Add Cleaning Crystals
Empty one packet of Invisalign crystal cleaners into the water. Stir until fully dissolved.
Step 3: Soak Aligners
Place your aligners into the solution and let them soak for 15 minutes.
Step 4: Brush and Rinse
After soaking, use a soft toothbrush to gently brush away loosened plaque. Rinse thoroughly with water before wearing again.
How Often Should You Clean with Crystals?
-
Daily deep clean with Invisalign cleaning crystals is recommended.
-
Between meals, you can simply rinse or brush with water.
-
Avoid harsh cleaning agents like mouthwash, bleach, or toothpaste, which can damage aligners.
Alternatives to Invisalign Aligner Cleaning System
Not every patient uses Invisalign’s official kit. Other effective options include:
-
Retainer cleaner tablet – affordable and widely available.
-
Generic aligner cleaners – often persulfate-free and safe.
-
Ultrasonic cleaners – for an extra deep clean.
Comparison: Invisalign Cleaning Crystals vs. Alternatives
| Cleaning Method | Pros | Cons | Cost |
|---|---|---|---|
| Invisalign cleaning crystals | Designed for aligners, safe, effective | Pricey, single-use packets | $$ |
| Retainer cleaner tablet | Affordable, easy to use, persulfate-free options | Some formulas may discolor | $ |
| Ultrasonic cleaner | Deep cleaning, reusable | Higher upfront cost | $$$ |
| Homemade cleaning (baking soda) | Cheap and natural | Not as effective for odor | $ |
Shocking Risks of a Dirty Invisalign: Could Your Neglect Lead to Serious Health Issues?
Skipping regular invisalign cleaning can turn it into a breeding ground for harmful bacteria, leading to infections, Bad breath, and even damage to your teeth and gums. This isn’t just about hygiene—it’s about protecting your health. Don’t wait until it’s too late.

Want to see exactly how to clean your retainer or aligner the right way?
We’ve added a quick video tutorial below to show you step-by-step how to remove bacteria, stains, and odor — without damaging your trays. Whether you're using Invisalign or a clear retainer, this visual guide makes it easy to follow along and keep your trays looking like new.
What Patients Are Saying
⭐️⭐️⭐️⭐️⭐️
“I switched from crystals to Weiss Naturals retainer cleaner tablets, and my aligners are crystal-clear every day. Easy to use and much cheaper!” – Emily R.
⭐️⭐️⭐️⭐️⭐️
“Love Weiss Naturals! No strong chemical smell, and my trays don’t get cloudy anymore. Totally recommend.” – James K.
👉 Check out Weiss Naturals reviews on Amazon here.

FAQs: Invisalign Aligner Cleaning System
How often should I use the Invisalign aligner cleaning system?
Once per day for best results, especially after eating or drinking colored beverages.
Can I use toothpaste to clean aligners?
No, toothpaste is too abrasive and can scratch aligners.
Are Invisalign cleaning crystals safe?
Yes, they are designed for aligners and won’t cause discoloration or damage.
What’s the best alternative to crystals?
A persulfate-free retainer cleaner tablet is the most affordable and effective alternative.
Final Thoughts
The Invisalign aligner cleaning system is effective, but not your only option. While Invisalign cleaning crystals keep trays clear, alternatives like retainer cleaner tablets or ultrasonic cleaners can be just as effective—and often more budget-friendly.
Disclaimer:
The content in this article is for informational purposes only and is not a substitute for professional medical advice. Always consult with a healthcare provider before making any changes to your health regimen. The author and publisher do not take responsibility for any consequences resulting from the information provided in this article.

Meet Dr. Jessica Cohen
Dr. Jessica Cohen, DMD, MS is a Board-Certified Orthodontist serving the Deerfield area with over a decade of experience. As a devoted mom to three girls — Scarlett, Shiloh, and Schuyler — she knows the value of creating a warm, welcoming environment for patients of all ages. Passionate about crafting confident, healthy smiles, Dr. Cohen blends science and artistry through her background in studying the esthetics of beauty pageant winners. She proudly recommends Weiss Naturals Persulfate-Free Retainer Cleaner tablets by B. WEISS to her patients — and even her own kids use it daily— for its gentle yet effective formula that keeps retainers fresh without harsh chemicals. It’s her trusted solution for safe, everyday care.
Related product

Meet Dr. Jessica Cohen
Dr. Jessica Cohen, DMD, MS is a Board-Certified Orthodontist serving the Deerfield area with over a decade of experience. As a devoted mom to three girls — Scarlett, Shiloh, and Schuyler — she knows the value of creating a warm, welcoming environment for patients of all ages. Passionate about crafting confident, healthy smiles, Dr. Cohen blends science and artistry through her background in studying the esthetics of beauty pageant winners. She proudly recommends Weiss Naturals Persulfate-Free Retainer Cleaner tablets by B. WEISS to her patients — and even her own kids use it daily— for its gentle yet effective formula that keeps retainers fresh without harsh chemicals. It’s her trusted solution for safe, everyday care.