A Joint Commission surveyor walks into your endoscopy unit unannounced. She pulls a reprocessing log from last Tuesday, checks the chemical monitoring record, and asks the technician on duty to walk through the disinfection sequence for a flexible bronchoscope. Within ten minutes, she has identified three documentation gaps and one step performed out of order. Your unit now has a finding and an action plan due in 60 days.
This scenario is not hypothetical. It is happening in hospitals across the country, and the data behind it should concern every endoscopy director and OR leader responsible for infection prevention. The Joint Commission's own survey data shows the standard covering high-level disinfection and sterilization was the single most frequently cited noncompliant requirement across all U.S. hospital surveys conducted in 2023.
This article breaks down the most common reprocessing errors driving those findings, explains what regulators look for during a survey, and provides a practical workflow framework you can implement in your endoscopy program.
Reprocessing has always been a demanding, detail-heavy process. What has shifted is how closely regulators are watching it, and how fast the expectations are moving.
The industry standard, AAMI ST91, was updated in 2021 for the first time in seven years, adding requirements like visual inspection under magnification and tighter drying and storage protocols. The FDA has also issued safety communications on specific scope types, signaling that regulators expect facilities to update their practices as new guidance is issued, rather than waiting for the next survey to catch them off guard.
Even professional societies acknowledge the gap. The ASGE multisociety guideline notes that compliance with published standards varies widely across facilities, which tracks with what internal audits tend to show: written policy and daily practice do not always match.
That gap has a price. One 2024 study found full compliance with the updated standard adds real time and cost to every procedure. But weigh that against the cost of a survey finding, a patient notification, or case delays rippling through the schedule, and the added minutes look like the cheaper option.
Noncompliance is not usually the result of one dramatic failure. It is the accumulation of small, repeated breakdowns across the reprocessing cycle, each one individually minor but collectively dangerous. A 2023 evaluation of HLD practices in an ambulatory urology setting documented the specific types of errors that drive findings. If any of these sound familiar, you are not alone.
Skipped or Inadequate Precleaning
Point-of-use precleaning, wiping, and suctioning the endoscope immediately after the procedure is the first and most critical step. When it is missed or delayed, bioburden dries inside channels and on surfaces. Dried organic material is the single biggest obstacle to effective HLD. No amount of downstream processing reliably compensates for a scope that sat uncleaned for 20 minutes on a transport cart.
Incomplete Documentation
This is what surveyors look for first, because it is the easiest to verify. Missing records of materials used, contact times, chemical concentration testing, lot numbers, and technician identification create an immediate gap in documentation. If the record does not show the step was done, a surveyor will treat it as if it was not done.
Omission of Proper Disinfectant Flushing
Channels that are not thoroughly flushed during the cleaning and disinfection process retain residual organic material. That residual compromises the efficacy of HLD. This is a procedural step requiring staff time and attention. Understandably, both resources are often unavailable when case volume is high, and turnaround pressure is constant.
Storage Without Alcohol Rinse
Storing a reprocessed endoscope without a final alcohol rinse allows moisture to remain in channels. Moisture creates conditions for microbial growth and biofilm formation — effectively undoing the work of reprocessing. This step is often skipped when the focus is on getting scopes back into circulation quickly.
Lack of Training Documentation
Staff may be competent. They may have been trained thoroughly. But if there is no documented record of initial competency assessment, annual re-validation, or manufacturer-specific IFU training for each scope model in use, that competency does not exist from a surveyor's perspective. Missing training records are among the most common and most avoidable findings.
Visual Inspection Failures
AAMI ST91:2021 introduced a requirement for lighted magnification or borescope inspection of endoscope channels and components. Research by Ofstead and colleagues demonstrated that visual inspection with borescopes reveals residual contamination not visible to the unaided eye. Many facilities have not yet adopted this step or do not have the equipment to perform it consistently.
These errors are not random. They follow a pattern — time pressure compresses steps, documentation falls behind, training is assumed rather than verified, and inspection shortcuts become routine. The result is a facility that believes it is compliant but cannot demonstrate compliance under scrutiny. When left unchecked, these patterns contribute to instrument malfunctions and risks that affect both patient safety and operational continuity.
Understanding the specific items surveyors evaluate helps you prepare — and more importantly, helps you build systems that generate the evidence of compliance automatically, rather than scrambling to reconstruct it before a survey.
Joint Commission and CMS Focus Areas
Joint Commission and CMS surveyors examine a consistent set of elements during an endoscope reprocessing review. The ASC Quality Collaboration's Endoscope Reprocessing Toolkit outlines what CMS surveyors specifically look for:
The common thread is documentation that connects policy to practice. A well-written policy that does not match what a surveyor observes on the unit floor creates a finding just as quickly as having no policy at all.
FDA Expectations
The FDA expects compliance with device-specific reprocessing instructions and monitors adverse events through the MAUDE database. When the agency issues a safety communication — as it did for flexible bronchoscopes in 2021 and Karl Storz urological endoscopes in 2022 — it expects facilities to review, respond, and update their protocols accordingly. Failure to act on a safety communication is a documentation gap waiting to become a finding.
CDC/HICPAC Essential Elements Framework
The CDC, through its Healthcare Infection Control Practices Advisory Committee (HICPAC), published the Essential Elements of a Reprocessing Program for Flexible Endoscopes. This framework identifies five pillars of a compliant reprocessing program:
If your program cannot demonstrate strength across all five pillars, you have a structural vulnerability — not just a documentation gap.
What Triggers a Finding
Surveyors are trained to look for discrepancies. The most common triggers include:
The pattern is straightforward: if you cannot show it, you cannot claim it.
Compliance cannot depend on individual staff performance on individual days. It has to be built into the system — the sequence, the documentation, the training cadence, and the audit schedule. Here is a framework you can adapt to your endoscopy program.
Start with a master reference document that links each endoscope model in your inventory to its manufacturer's current reprocessing instructions. This is not a one-time exercise. It is a living document.
Define the required steps for your facility and make them non-negotiable. The standard sequence based on AAMI ST91:2021 and current guidance — including best practices in endoscope reprocessing — includes:
Build this sequence into a physical or digital checklist. Each step requires sign-off with technician identification and timestamp. The checklist is not optional — it is the documentation that demonstrates compliance.
Implement a tracking system to be paper-based or electronic, and captures the following information for every reprocessing cycle:
These records must be organized and retrievable. When a surveyor asks for the reprocessing history of a specific scope on a specific date, you need to produce it within minutes — not hours.
Training is not a one-time event. It is a documented, recurring cycle:
Every element must be documented and filed where it can be retrieved for surveyor review. SGNA Standards of Infection Prevention in Reprocessing reinforce the importance of adequate time allocation for both reprocessing and training — rushing either one creates risk.
A compliant program is not one that passes a survey. It is one that generates continuous evidence of compliance between surveys:
Auditing is not punitive. It is the mechanism that catches drift before a surveyor does. If your audits reveal persistent gaps that your internal team cannot close, it may be time to consider sterile processing consulting to bring in external expertise.
Building and sustaining a compliant reprocessing program requires consistent execution day after day, scope after scope, across every shift. That is exactly what Surgical Solutions delivers through its Endoscopy Support Services.
Surgical Solutions provides on-site, trained technicians embedded directly in hospital endoscopy units. These are not rotating contractors. They are dedicated team members who know your scope, workflows, and documentation requirements. Our comprehensive support services include scope reprocessing (HLD, cleaning, leak testing, and full documentation), scope service and preventive maintenance, biological monitoring, and storage management, which is the complete reprocessing lifecycle, managed with accountability.
The model addresses the root causes of noncompliance: inconsistent execution when staffing fluctuates, knowledge gaps when scope inventories change, documentation failures when volume spikes, and the training burden that falls on directors already stretched across multiple priorities.
The results are measurable. Facilities working with Surgical Solutions have documented a 79% reduction in monthly scope repairs and a 50% decrease in repair spend outcomes that reflect the downstream impact of consistent, proper handling across every step of the reprocessing cycle. See how one hospital achieved these results in our Transform Endoscopy Operations case study.
Endoscopy and OR directors ready to close the gap between reprocessing policy and daily practice are welcome to reach out.
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What Are the Steps for Endoscope Reprocessing?
The standard sequence includes point-of-use precleaning, leak testing, manual cleaning, visual inspection, HLD or sterilization, rinsing, drying, and proper storage. Each step must follow the manufacturer's IFU and be documented for compliance.
What Is the Difference Between HLD and Sterilization for Endoscopes?
HLD eliminates most pathogens except some bacterial spores, while sterilization eliminates all microbial life. AAMI ST91:2021 recommends sterilization for high-risk endoscopes when the device and facility infrastructure allow it.
How Long Can a Reprocessed Endoscope Be Stored?
The September 2025 Joint Commission multisociety guidance made no specific recommendation on storage duration limits. Follow your manufacturer's IFU and facility policy, and err toward reprocessing before use if the storage period is uncertain.
What Training Is Required for Endoscope Reprocessing Staff?
Staff must complete an initial competency assessment, annual re-validation, and manufacturer-specific IFU training for each scope model they process. All training and assessments must be documented and retrievable for surveyor review.
What Does the Joint Commission Look For in Endoscope Reprocessing?
Surveyors evaluate documented reprocessing protocols aligned with manufacturer IFU, staff competency records, chemical monitoring logs, storage conditions, and evidence of a quality assurance program. The focus is on whether written policy matches observed practice.