A flexible endoscope is only as safe as the last time it was reprocessed. It goes into the airway, the GI tract, or the urinary tract. It has narrow channels you can’t see into. It can’t go in the autoclave. That makes cleaning and disinfection the part of endoscopy that is easiest to get wrong and hardest to notice when it’s wrong.
Most of us learned to pass a scope long before anyone walked us through reprocessing it. The procedure gets the attention, and the cleanup gets whoever is free at the end of a long day. This guide covers the principles, the order of the steps, and the questions to ask when you buy a scope or train your team.
It’s a general overview, not a replacement for the instructions that came with your scope. Those always come first.
A note on where this guidance comes from
The most detailed guidance on reprocessing endoscopes is the CDC’s Guideline for Disinfection and Sterilization in Healthcare Facilities (Rutala et al., 2008). It’s written for human healthcare. We didn’t find an equivalent national standard written for veterinary practice, so we use the CDC guideline as a benchmark. Your scope manufacturer’s instructions for use govern your specific scope, and your provincial veterinary regulator may have requirements of its own.
Why flexible endoscopes need special attention
The CDC classifies endoscopes that touch mucous membranes as semicritical items. Its guidance is that these need, at a minimum, high-level disinfection after each patient (Rutala et al., 2008). Heat-sensitive endoscopes, such as gastrointestinal endoscopes and bronchoscopes, must be properly cleaned and given at least high-level disinfection after each use (Rutala et al., 2008).
Two reasons make flexible scopes a special case. First, because of the body cavities they enter, they pick up high levels of microbial contamination every time they’re used (Rutala et al., 2008). Second, they can’t be steam sterilized, so you’re relying on a chemical or low-temperature process to finish the job.
It helps to know what high-level disinfection means. The CDC says it can be expected to destroy all microorganisms, although when high numbers of bacterial spores are present, a few spores might survive (Rutala et al., 2008). That’s why the step before it matters so much.
Step 0: Leak test every time
The CDC recommends testing each flexible endoscope for leaks as part of every reprocessing cycle (Rutala et al., 2008). It also recommends leak testing before the scope is immersed (Rutala et al., 2008). If a scope fails the leak test, take it out of clinical use and have it repaired.
The reason is simple. A leak lets fluid reach parts of the scope that were never meant to get wet, which can damage it and make proper reprocessing impossible. A scope that passes a leak test on Monday can fail on Thursday, which is why the test belongs in every cycle and not just the first one.
The five steps
The CDC describes endoscope disinfection with a liquid chemical agent as five steps, after leak testing (Rutala et al., 2008).
1. Clean. Mechanically clean the inside and outside of the scope, including brushing the internal channels and flushing each channel with water and a detergent or enzymatic cleaner (Rutala et al., 2008). Cleaning is necessary before both manual and automated disinfection, and the CDC notes that it reduces microbial contamination by 4 to 6 log10 (Rutala et al., 2008). Disinfectant can’t reach what debris is still covering, so a skipped or rushed cleaning step undermines everything after it.
2. Disinfect. Fully immerse the scope in a high-level disinfectant or chemical sterilant, making sure all channels are filled (Rutala et al., 2008).
3. Rinse. Rinse the scope and all channels with high-quality water (Rutala et al., 2008). The CDC lists sterile water, filtered water, or tap water that meets clean water standards as options, depending on the setting.
4. Dry. Rinse the insertion tube and channels with alcohol, and dry them with forced air before storage (Rutala et al., 2008). The CDC identifies drying as essential to greatly reduce the chance of the scope being recontaminated by waterborne organisms (Rutala et al., 2008).
5. Store. Store the scope in a way that protects it from damage and contamination and promotes drying (Rutala et al., 2008). The CDC’s example is hanging it vertically.
Use the contact times, concentrations, and products your scope’s manufacturer specifies. This article doesn’t give them, because they vary by product and by scope.
Manual or automated reprocessing
Some practices clean and disinfect by hand. Others use an automated endoscope reprocessor, often called an AER. If you use one, the CDC says to place the scope in the reprocessor and attach all the channel connectors according to the AER manufacturer’s instructions, so that every internal surface is exposed to the disinfectant (Rutala et al., 2008). A reprocessor doesn’t replace the cleaning step. The CDC is clear that cleaning is necessary before automated disinfection too (Rutala et al., 2008).
If the scope manufacturer’s instructions and the reprocessor manufacturer’s instructions disagree, the CDC advises comparing them and resolving the conflict by contacting both manufacturers (Rutala et al., 2008).
Choosing chemicals and methods
- Use an approved high-level disinfectant or sterilant. Choose one authorized in your country and approved by your scope’s manufacturer. The CDC advises avoiding any chemical the manufacturer warns against, because it can damage the scope (Rutala et al., 2008).
- Soaking agents are not all equal. AAHA’s overview of sterilization methods notes that most agents used for soaking are high-level disinfectants, not true sterilization agents. The one exception it names is endoscopy equipment that doesn’t tolerate autoclaving, where high-level disinfectants like glutaraldehyde may be used (American Animal Hospital Association [AAHA], n.d.).
- Ethylene oxide is uncommon for flexible endoscopes. The CDC notes it requires long processing and aeration time (about 12 hours) and is a potential hazard to staff and patients (Rutala et al., 2008).
- Plasma sterilization is another option for some heat-sensitive devices. AAHA’s overview describes hydrogen peroxide gas plasma as a faster, non-carcinogenic alternative that needs no venting, but it can’t be used with wood, paper, linen, or gauze. It describes air plasma as having a four-hour cycle (AAHA, n.d.). Whether either is right for your scope depends on the manufacturer.
Drying and storage deserve their own attention
Drying is the step teams cut when the day runs late. The CDC treats it as one of the most important, because moisture left in a channel gives organisms a place to grow (Rutala et al., 2008). Build it into the routine: the alcohol flush, then forced air, then hanging the scope vertically in a space that protects it from damage and contamination.
People and paperwork
The CDC recommends giving anyone assigned to reprocess endoscopes device-specific reprocessing instructions, so they know how to clean and disinfect that exact scope (Rutala et al., 2008). A procedure written for one scope may not fit another. In practice that means:
- A written, scope-specific procedure kept where reprocessing happens
- Training for every team member who reprocesses, with a refresher when a new scope arrives
- A log for each cycle
- Optionally, random bacterial surveillance cultures of processed scopes, which the CDC says facilities can consider as part of a quality program (Rutala et al., 2008)
A log you can adapt
Consider recording these fields for each cycle. Adjust them to your manufacturer’s instructions:
- Date and time
- Scope name and serial number
- Patient or procedure (according to your records policy)
- Leak test result (pass or fail)
- Cleaning completed (initials)
- Disinfectant or method used, and the contact time recorded
- Rinse and dry completed (initials)
- Storage location
- Name of the team member who reprocessed
Where reprocessing goes wrong
Based on the guidance above, these are the points to watch:
- Skipping the leak test because the scope looked fine
- Disinfecting before cleaning, or rushing the brushing and flushing
- Using a chemical the manufacturer warns against, which can damage the scope
- Not drying the channels, then storing the scope while it’s still damp
- Relying on a general procedure instead of device-specific instructions
- Continuing to use a scope that failed a leak test
What to ask before you buy a scope
- Can I get the manufacturer’s reprocessing instructions before I buy?
- Which cleaning agents and disinfectants are approved for this scope, and which are not?
- Is a leak tester included, and what does it fit?
- Which low-temperature sterilization methods, if any, does the manufacturer approve?
- What does the warranty cover, and does it cover damage from fluid ingress?
- Is a loaner available if the scope needs repair?
We carry Aohua veterinary endoscopes, including the VET-6028R video endoscope (1,500 mm working length, 6.0 mm distal end, 2.8 mm instrument channel) and the OR-160 touch screen video processor. You can see everything on our veterinary endoscopes page. For more on choosing a scope, see Top Things to Know Before Investing in a Veterinary Endoscope, Top 5 Veterinary Endoscopes, and our overview of endoscopy for diagnostics and treatment.
When a scope fails its leak test, or something looks wrong
Don’t use it. Our repair team provides phone support and repairs, our inspection service covers preventative maintenance, and the Just Works service plan puts it on a schedule. Financing is available, and you can request a quote for any scope or accessory. For the instruments that can be steam sterilized, see our guide to choosing a veterinary autoclave.
Frequently asked questions
Do I need to leak test my endoscope every time? The CDC recommends testing each flexible endoscope for leaks as part of each reprocessing cycle, and removing from use any scope that fails (Rutala et al., 2008).
Can I autoclave a flexible endoscope? Flexible endoscopes are generally heat-sensitive, so they’re typically cleaned and high-level disinfected, or sterilized by a low-temperature method the manufacturer approves (Rutala et al., 2008). Don’t autoclave one unless the manufacturer says it’s safe.
What does high-level disinfection mean? The CDC says it can be expected to destroy all microorganisms, although when high numbers of bacterial spores are present, a few spores might survive (Rutala et al., 2008).
Why does drying matter so much? The CDC identifies drying as essential to greatly reduce the chance of recontamination by waterborne organisms, which is why it recommends an alcohol rinse and forced air before storage (Rutala et al., 2008).
How should I store an endoscope? In a way that protects it from damage and contamination and promotes drying. The CDC gives hanging it vertically as an example (Rutala et al., 2008).
Does an automated reprocessor replace manual cleaning? No. The CDC says cleaning is necessary before both manual and automated disinfection (Rutala et al., 2008).
What if the scope and reprocessor instructions disagree? The CDC advises comparing the two sets of instructions and resolving any conflict by contacting both manufacturers (Rutala et al., 2008).
Is there a veterinary standard for reprocessing? We didn’t find a national standard written for veterinary practice. The CDC guideline is a useful benchmark, your scope’s instructions for use govern, and your provincial regulator may have requirements of its own.
References
American Animal Hospital Association. (n.d.). Sterilization methods in vet med: Not one size fits all. Trends Magazine. Retrieved November 14, 2026, from https://www.aaha.org/trends-magazine/publications/sterilization-methods-in-vet-med-not-one-size-fits-all/
Rutala, W. A., Weber, D. J., & Healthcare Infection Control Practices Advisory Committee. (2008). Guideline for disinfection and sterilization in healthcare facilities, 2008 (Last update: May 2019). Centers for Disease Control and Prevention. https://www.cdc.gov/infection-control/media/pdfs/guideline-disinfection-h.pdf