What should I use to clean and disinfect my reptile's enclosure?

Person Cleaning Reptile Enclosure

Keeping your reptile’s habitat clean and tidy will go a long way towards preventing illnesses and promoting your companion’s health and wellbeing. It can be hard to determine what cleaning products to use with exotic pets like reptiles, though.

What’s safe?

What’s toxic?

What works???

First, let’s review the basics:

  • Cleaning your reptile’s cage involves removing organic debris and residue. Doing so will keep the habitat looking tidy, reduce harmful microorganisms, prevent or minimize foul odors, improve the air quality, and prevent bacterial or fungal overgrowth. Spot-cleaning, scrubbing decorations, spraying and wiping down surfaces, and substrate changes are all examples of cleaning your pet’s home. Thoroughly cleaning the enclosure and decorations involves using soap, detergent, or another cleaning agent designed to loosen, dissolve, or even repel dirt and oil molecules.
  • Disinfecting your companion’s enclosure involves using a chemical classified as a disinfectant. Disinfectants kill various harmful microorganisms, like bacteria, viruses, and fungi. Some disinfectants kill nearly all problematic organisms, while others might only work against certain types. The presence of organic matter inactivates many disinfectants - that means if you don’t clean the poop, urate, food, and skin residue first, the disinfectant won’t kill any microorganisms.

Now that you know the difference let’s learn about common and helpful cleaners and disinfectants for our reptiles’ homes.


Vinegar is an acidic solution that works by dissolving mineral deposits, dirt, and oils. It’s an excellent deodorizer, and it leaves terrarium glass with a streak-free shine. You’ll probably need a stronger cleanser - like soap - to completely remove organic material before you try to disinfect anything.

Exo Terra’s Glass Cleaner is a similarly acidic cleaning agent. It’s a gel rather than a liquid, which facilitates prolonged contact with those particularly stubborn water stains.


In simplified terms, soap is a cleaning agent created by combining water with certain types of fat (ex.: lard) and a basic, or alkali, salt (ex.: lye). Compared to disinfectants, it’s pretty safe, natural, and environmentally friendly.

Soap may reduce the concentration of microorganisms by helping to rinse them away, and it does a stellar job of removing organic debris - which is necessary before using most disinfectants. Grease, blood, feces, or food residue will neutralize many disinfecting agents.

Dawn dish soap is a classic and readily available soap that’s safe for reptiles. Zilla’s Terrarium Cleaner and Exo Terra’s Terrarium Decor Cleaner are soaps formulated and safe for use around reptiles.


Chlorine bleach is a widely-available and well-known oxidizing disinfectant. It’s a popular household cleaning agent because it’s effective against most pathogens.

Unfortunately, it’s not very safe. Chlorine bleach can cause burns if it comes into contact with bare skin, and the fumes irritate mucous membranes and the respiratory system.

If you’re going to use chlorine bleach, it’s imperative to:

  • Temporarily house your reptile in another room
  • Open windows, run a fan and do whatever else you can to increase ventilation
  • Wear rubber cleaning gloves, safety goggles, and a face mask
  • Dilute the bleach: Use ⅓ cup of bleach per gallon of water
  • Rinse all surfaces thoroughly with clean water and allow them to air dry completely before your reptile comes in contact
    • You shouldn’t be able to smell any bleach in the room if it’s ready for your reptile

Hydrogen Peroxide

A safer oxidizing disinfectant alternative is hydrogen peroxide. Household hydrogen peroxide is readily available in a 3% solution, so there’s no need to dilute it more than that - pour it straight into a spray bottle and get to work!

3% hydrogen peroxide doesn’t release irritating fumes or odors and can safely come into contact with skin. It’s the only disinfectant that’s highly effective against most protozoan parasite oocysts - to successfully tackle reptile-specific Cryptosporidium species, you’ll need to find a supplier of 6% hydrogen peroxide.


Isopropyl alcohol is another readily available household disinfectant with a wide safety margin, even around our sensitive reptilian companions.

The great thing about rubbing alcohol, as it’s commonly known, is that you don’t need to rinse it away - it will evaporate on its own. Once you no longer smell alcohol, the surface is safe for your pet.

The drawback is that alcohol NEEDS prolonged contact with a surface to work as a disinfectant. In other words, you can’t simply spray it on and immediately rinse or wipe it away. We’re talking about a minimum of 20 minutes of surface contact for stubborn microorganisms.

Household concentrations of isopropyl alcohol (typically 70% or 91%) are appropriate for disinfecting small surfaces - don’t dilute them any further. They’re also great for cleaning glass without leaving streaks.


Chlorhexidine is a popular antiseptic and disinfectant. That means it’s safe to come into contact with living critters - like you or your lizard! It’s effective against a wide range of bacteria and viruses. There aren’t any toxic fumes to worry about, and you don’t have to rinse it away.

Follow package instructions for diluting it to the proper concentration for disinfection (10% concentration) - or even as an antiseptic wound wash (1% concentration)! Nolvasan is the common brand name, but many other companies distribute their own solutions at various concentrations.


Povidone-iodine is a popular antiseptic and surgical scrub that also functions as a mild disinfectant. It’s primarily effective against bacteria but also eradicates some viruses.

Iodine is non-toxic but may leave surface stains and dry your skin if you don’t wear gloves. No need to dilute a household 10% povidone-iodine solution any further.

Quaternary Ammonium

Quaternary ammonium compounds aren’t as popular because they’re generally less effective and more dangerous than the other options listed above. Zoo Med Wipe Out is one reptile-specific quaternary ammonium disinfectant that is safer to use around our cold-blooded pets.

An exception to this rule is the veterinary disinfect F10. F10’s proprietary formula produces no hazardous fumes or residues, can safely come into contact with skin, and is one of the most comprehensive disinfectants on the market.

Unfortunately, F10 can be a challenge to find, and it’s pretty pricey. Still, if you’re worried about eradicating some of the most resilient and problematic pathogens in the reptile hobby - F10 should be the primary weapon in your arsenal. Follow package directions for dilution instructions, depending on your target microorganism.

Best Reptile Disinfectant

There’s no single BEST reptile disinfectant. Choose the best disinfectant for your situation based on factors like:

  • Safety
  • Availability
  • Volume needed
  • Budgetary considerations
  • The microorganism (s) you’re targeting

Of particular importance is learning about the chemical type, concentration level, and contact time needed to kill the specific microorganism you’re trying to eradicate. What kills some pathogens will not kill others. Here’s a handy chart if you’re waging war against one particular diagnosed microorganism.

Please note: products check-marked are suggested by veterinary professionals and usually proven to be effective against the specific pathogen in question in scientific studies, but many of these disinfectants are likely effective against much more than what’s shown.

Whatever cleaning and disinfecting solution or combination you decide to use, we hope this has helped you make an educated decision that will keep your beloved reptile safe and healthy!

Chlorine Bleach Hydrogen Peroxide Isopropyl Alcohol Chlorhexidine Povidone-Iodine F10SC
Infection-Causing Bacteria
(Mouth Rot, Scale Rot,
Respiratory Infections, etc.)
Wasting Disease, ADV,
Stargazing Disease

(Cryptosporidium spp.)

*6% concentration
Fer-de-Lance virus,
Ophidian Paramyxovirus

Reptilian ferlavirus)
Inclusion Body Disease, IBD
Reptile Nidovirus
Mite Eggs
Hirstiella spp)
Strongyloides spp, Rhabdias spp,
Physaloptera spp, Kalicephalus spp, etc.)
Onygenalean Dermatomycoses,
Yellow Fungus Disease

Snake Fungal Disease
Ophidiomyces ophiodiicola)


"The Antimicrobial Spectrum of Disinfectants." The Center for Food Security and Public Health, https://www.cfsph.iastate.edu/pdf/antimicrobial-spectrum-of-disinfectants.

"Disinfectants and Their Uses." Beautiful Dragons Reptile Rescue, http://www.beautifuldragons.com/Disinfectants.html.

Divers, Stephen J. "Disorders and Diseases of Reptiles." Merck Veterinary Manual, August 2020, https://www.merckvetmanual.com/all-other-pets/reptiles/disorders-and-diseases-of-reptiles.

"Infectious Disease Manual: Infectious Diseases of Concern to Captive and Free Ranging Wildlife in North America." The American Association of Zoo Veterinarians
Animal Health and Welfare Committee, April 2020, https://cdn.ymaws.com/www.aazv.org/resource/resmgr/idm/idm_updated_april_2020.pdf.

Roscoe, Eric ad Mede, Erica. "Keeping It Clean: Cleaning and Disinfecting Your Reptile or Amphibian’s Enclosure." Madison Area Herpetological Society, https://madisonherps.org/kickstart/en/wisconsin-reptile-resources/education-articles/106-keeping-it-clean-cleaning-and-disinfecting-your-reptile-or-amphibian-s-enclosure.

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