How to Clean Medical Instruments: Step-by-Step Guide

Important: This article provides general educational guidance for reusable medical and surgical instruments. It does not replace the instrument manufacturer’s instructions for use (IFU), the cleaning chemistry manufacturer’s directions, or a healthcare facility’s validated reprocessing procedures.

On this page

• Why instruments must be cleaned before sterilization
• The 8-step overview
• Point-of-use care and safe transport
• PPE and the decontamination area
• Manual cleaning
• Ultrasonic cleaning
• Mechanical and automated cleaning
• Hinges, ratchets, serrations and lumens
• Cleaning solutions and chemistries
• Rinsing and drying
• Inspection and cleaning verification
• Cleaning vs disinfection vs sterilization
• Instruments vs medical equipment
• Common mistakes
• Frequently asked questions

Cleaning medical instruments is the first stage of reprocessing and the one every later stage depends on. If soil is left on an instrument, disinfection and sterilization cannot be relied upon to work.

This guide explains how to clean reusable medical instruments and surgical instruments step by step: point of use care, transport, manual and mechanical cleaning, rinsing, drying and inspection before the next validated stage. It applies to reusable hand held instruments made from surgical grade stainless steel and similar materials. Always follow the IFU supplied with the specific instrument and your facility’s validated procedures.

Why Medical Instruments Must Be Cleaned Before Sterilization

Medical instruments must be cleaned before disinfection or sterilization because organic and inorganic residue left on the surface interferes with the effectiveness of those processes.

The material being removed is soil blood, tissue, bone fragments and other organic or inorganic residue. Soil physically shields the microbial population on an instrument, known as its bioburden, from the sterilant. An instrument that looks acceptable but has not been properly cleaned can pass through a full sterilization cycle and still be unsafe.

Timing matters. CDC guidance notes that soil which dries or bakes onto an instrument becomes considerably harder to remove, and makes the disinfection or sterilization process less effective or ineffective. This is why cleaning begins in the procedure room, not in the decontamination area.

Cleaning also protects the instrument. Blood and saline left on stainless steel cause staining, pitting and corrosion. Instruments cleaned promptly and inspected regularly keep their cutting edges, alignment and ratchet action for longer, which directly affects how they perform in a procedure

How to Clean Medical Instruments: 8-Step Overview

Cleaning medical instruments follows the same sequence for most reusable devices: treat at the point of use, transport safely, open or disassemble, clean, rinse, dry, inspect, then proceed to the required downstream process. Each step is explained in detail below.

1. Point-of-use treatment  remove gross soil and keep the instrument moist so nothing dries on it.
2. Safe transport  move instruments to the decontamination area in a closed, leak-proof container.
3. Open or disassemble  unlock ratchets and separate any instrument the IFU says is separable.
4. Clean manually  friction and fluidics, using a method the IFU allows.
5. Clean mechanically where appropriate  ultrasonic cleaning or an automated washer, if the device is compatible.
6. Rinse  remove all cleaning chemistry and loosened soil with water of the quality your process specifies.
7. Dry and inspect  dry thoroughly, including lumens and hinges, then check cleanliness and function.
8. Prepare for the next stage  package for the validated disinfection or sterilization process that applies to that device.

Point-of-Use Care and Safe Transport

Point of use treatment means dealing with soil immediately after a procedure, before it dries, and moving instruments to the decontamination area in a contained way.

Gross soil is wiped away, lumens may be flushed where the IFU allows, and instruments are kept moist until they reach the decontamination area. A moisture-retaining product intended for the purpose, or another method your facility has validated, keeps soil removable. Instruments should be opened and unlocked at this stage rather than closed on soil.

Transport instruments in a closed, leak proof, clearly identified container. Sharps should be contained so staff are not exposed while handling the tray. Heavy instruments should not be piled on top of fine or delicate patterns that is how tips and micro instruments get bent in transit. Sterilization trays and baskets designed for the purpose make this straightforward; see our sterilization baskets range.

PPE and the Decontamination Area

Cleaning belongs in a designated decontamination area, and the person doing it needs protection appropriate to the exposure involved.

The decontamination area of a sterile processing department also called the SPD or CSSD exists to keep contaminated instruments, aerosols and splashes away from clean areas and from patient care. Full cleaning should happen there rather than being finished casually at the point of care.

Handling soiled instruments means potential exposure to blood, tissue and cleaning chemistry. Personal protective equipment for this work typically includes a fluid resistant gown or apron, heavy duty gloves, and eye and face protection against splashing. Follow your facility’s exposure control plan for the specific requirements.

This is not a side note. Several practices later in this guide brushing below the waterline, using low foaming detergent so the sink bottom stays visible, containing sharps exist primarily to protect the person doing the cleaning.

Manual Cleaning of Surgical Instruments

Manual cleaning works through two mechanisms: friction, meaning brushing or scrubbing the soiled surface, and fluidics, meaning fluid under pressure to reach channels a brush cannot.

CDC guidance identifies these as the two essential components of manual cleaning. Friction handles accessible surfaces. Fluidics handles internal channels after brushing, and any channel whose design will not allow a brush to pass through at all. Most cleaning failures come from using only one where both were needed.

Start with a cool-water rinse

An initial cool or cold-water rinse helps remove blood and any point-of-use pretreatment residue without promoting the protein coagulation that makes soil harder to remove. Hot water at this stage can set blood proteins onto the surface. Follow the device and cleaning-system IFUs for the required water temperature this is one parameter that genuinely varies by process.

Facilities with a three-bay sink use the first bay for this cool pre-rinse, the second for immersion and brushing in the cleaning solution, and the third for the final treated rinse.

Brushing

For immersible instruments, brush below the waterline. Brushing at the surface creates aerosols and sprays contaminated droplets around the work area, which is both a safety issue and a contamination risk. Where the IFU does not permit immersion, follow the non-immersion method it specifies instead.

Use a brush sized for the feature you are cleaning, and a soft brush on delicate tips and coatings. Open every hinged instrument and clean the box lock, serrations and ratchet teeth specifically, because that is where soil collects. Do not use steel wool or abrasive pads on stainless steel: they damage the passive surface layer and make the instrument more likely to corrode later.

Prepare the cleaning solution at the dilution and temperature stated by the chemistry manufacturer, and change it when it becomes soiled rather than working on through a whole tray. Low-foaming detergents are preferred so you can see into the sink and avoid injury from sharp instruments.

Ultrasonic Cleaning of Medical Instruments

Ultrasonic cleaning uses acoustic energy to create cavitation in a cleaning solution, lifting soil from surfaces a brush cannot reach — but it is fine cleaning, not a replacement for the rest of the process.

High-frequency sound waves propagated through the solution form tiny bubbles that implode against instrument surfaces, disrupting the bonds holding soil in place. This makes ultrasonic cleaning useful for box locks, hinges, serrations and other fine features. Gross soil should still be removed first, and instruments still need rinsing, drying and inspection afterwards.

Not every instrument or material is suitable. Some coatings, some dissimilar-metal assemblies, and many powered or electronic devices should not be processed this way. Confirm suitability in the instrument IFU before loading, and follow the ultrasonic unit’s own IFU for solution type, fill level, degassing and cycle time. Do not adopt a frequency, temperature or cycle length from a general article those come from the equipment.

Two risks are worth knowing. CDC notes that used ultrasonic cleaning solutions can carry bacterial contamination, since such solutions generally make no antibacterial label claims, and that the cleaning fluid can leave endotoxin on instruments, which has been associated with severe inflammatory reactions. Both are arguments for changing solution as specified and rinsing thoroughly afterwards.

Mechanical and Automated Cleaning

Automated cleaning equipment gives more consistent, reproducible results than hand scrubbing, which is why most sterile processing departments use it for the bulk of their instruments.

The common categories are distinct pieces of equipment, not interchangeable terms:

• Ultrasonic cleaners  fine cleaning by cavitation, covered above.
• Washer-decontaminators and washer-disinfectors  circulate water and detergent through spray arms, usually with a thermal rinse phase that provides a level of disinfection.
• Washer-sterilizers modified steam sterilizers that clean and then run a short steam cycle.

Cleaning performance in a washer-disinfector depends on four cycle parameters: time, temperature, chemistry and impingement impingement being the mechanical force of the spray arms. A machine with low impingement may need a more aggressive chemistry to compensate; a high-impingement machine relies on water pressure to shift soil. The correct settings come from the validated cycle, the washer IFU and the IFUs of the devices being processed.

Loading matters as much as the cycle. CDC guidance is specific: hinged instruments should be opened fully so the detergent solution reaches all surfaces, instruments should not be stacked, and devices should be disassembled as far as the IFU permits. An overcrowded tray is one of the most common causes of a cleaning failure that is not discovered until inspection.

Cleaning Hinges, Ratchets, Serrations and Lumens

Hinges, ratchets, serrations and lumens are where cleaning most often fails, because soil sits where it is hard to see and hard to reach. Each needs deliberate attention rather than a general wipe-down.

Box locks and hinges. Open the instrument fully, clean into the joint from both sides, and work the instrument open and closed while it is submerged so the joint is flushed through.

Ratchets and serrations. Brush along the grooves rather than across them, so the bristles reach the base of each groove.

Lumens and cannulated instruments. This is where friction and fluidics have to work together. Use a brush of the correct diameter and full working length and pass it all the way through — a brush that is too small will travel down the channel without ever touching the wall. Then flush the channel to carry out what the brush has loosened. Where a channel is too narrow or too convoluted for any brush, flushing under pressure is the only mechanism available, and the IFU should specify the method.

Tips and jaws. Clean fine tips gently and individually. Toothed jaws, rasps and files hold soil between the teeth and need a brush rather than a cloth.

Cleaning Solutions and Chemistries for Medical Instruments

There is no single cleaning solution that is correct for every reusable medical instrument — the right choice depends on the soil, the instrument material and what the IFU permits.

Neutral or near-neutral pH detergents are the most widely used, because they offer the best material compatibility profile while still removing soil effectively. Enzymes are often added to assist with organic material. Different enzyme classes do different jobs: proteases break down proteins such as blood and pus, lipases act on fats, and amylases act on starches.

One point is frequently misunderstood: enzymatic cleaners are not disinfectants. They are cleaning agents, and proteinaceous enzymes can actually be inactivated by germicides. They must also be rinsed off thoroughly, because residual enzyme detergent left on an instrument can cause a tissue reaction in the next patient.

Alkaline-based agents dissolve protein and fat residues efficiently and are used for medical device processing, but they carry a higher corrosion risk depending on the material. The evidence on which chemistry cleans best is genuinely mixed: some studies found enzymatic cleaners more effective than neutral detergents, while more recent work found no meaningful difference between enzymatic and alkaline-based cleaners. In practice, compatibility and correct use matter more than the category.

Three things decide whether a chemistry is appropriate

• Device and material compatibility. The instrument IFU states which chemistries may be used. Aluminium, titanium, coated surfaces and plated instruments are more restrictive than plain stainless steel.
• Concentration and contact conditions. Follow the dilution, temperature and contact time the chemistry manufacturer specifies. Stronger is not better, and an under-diluted solution can damage instruments.
• Water quality. Hardness and mineral content affect cleaning performance and the spotting or staining you see afterwards. Many facilities use treated water for the final rinse.

What not to use on surgical instruments

Household and general-purpose cleaning products are a common source of damage, and several of them are specifically worth naming:

• Bleach and chlorine-containing products. Chloride attacks stainless steel, causing pitting and corrosion that cannot be reversed. Bleach is a disinfectant, not an instrument cleaner, and it does not remove soil.
• Hydrogen peroxide as a general substitute. Some peroxide-based formulations are made for device processing, but a household peroxide bottle is not one of them and is not a cleaning agent for instruments.
• Vinegar, descalers and strong acids. Acidic products not intended for instruments attack the passive surface layer that protects stainless steel.
• Dish soap and general detergents. Not formulated or validated for medical device reprocessing; they can leave residues and are not designed to be rinsed to the required standard.
• Abrasive cleansers, scouring powders and steel wool. These scratch the surface and make future corrosion more likely.
• Saline left in contact with instruments. A frequent and avoidable cause of pitting.

Never mix cleaning or disinfecting chemicals unless the manufacturer explicitly instructs that combination. Some mixtures produce hazardous gases; others simply inactivate each other.

One safety note for the people doing the work: detergent enzymes can cause asthma or other allergic effects in users. This is another reason for appropriate PPE and adequate ventilation in the decontamination area.

Rinsing and Drying Medical Instruments

Rinsing removes cleaning chemistry and loosened soil; drying prevents water spotting, staining and corrosion. Both come after cleaning and before packaging, not after a packaged instrument has been sterilized.

Rinse thoroughly enough that no residue remains in hinges, serrations or lumens. Where the process specifies treated water for a final rinse, use it. Ordinary tap water can leave mineral deposits that look like staining and are often mistaken for rust. Water quality for the final rinse is typically controlled for hardness, chloride content and microorganisms, each for a different reason.

Dry instruments completely, including lumens, which usually need forced or filtered air rather than time on a tray. Moisture left in a box lock or a cannula causes corrosion and can interfere with sterilization. Instruments should be dry when they are inspected, because water hides exactly the kind of residue you are looking for.

Inspecting Instruments After Cleaning

Every instrument should be inspected after cleaning and drying and before the next stage, checking two separate things: whether it is actually clean, and whether it still works correctly.

Inspect under good light, and use magnification for fine tips, serrations and micro instruments. Look into box locks, ratchet teeth, serrations and lumen openings rather than only at the outer surface.

Lubricate hinged instruments where the IFU calls for it, using a lubricant intended for surgical instruments and compatible with your sterilization process.

Cleaning verification beyond visual inspection

Some facilities go further than visual checks. Cleaning process indicators change appearance once washer cycle parameters have been achieved, and residual soil testing methods such as ATP bioluminescence or protein detection give a measurable pass or fail rather than a judgement call.

These are useful for validating that a process is working consistently over time. It is worth knowing, though, that CDC states no real-time test exists that can verify cleaning in a clinical setting, and that at minimum every instrument should be individually inspected and visibly clean. Verification tools supplement that minimum; they do not replace it.

Cleaning vs Disinfection vs Sterilization

Cleaning physically removes soil, disinfection reduces microorganisms to a specified level, and sterilization is a validated process intended to eliminate all viable microorganisms. Cleaning always comes first.

Which process a device needs: the Spaulding classification

The level of processing required depends on how the device is used. The Spaulding classification sorts devices into three tiers by infection risk:

• Critical — enters sterile tissue or the vascular system. Requires sterilization. Most surgical instruments fall here.
• Semi-critical — contacts mucous membranes or non-intact skin. Requires at minimum high-level disinfection.
• Noncritical — contacts intact skin only. Requires low-level disinfection.

Because surgical instruments are almost always critical items, thorough cleaning followed by a validated sterilization process is the standard path. 

Two points are worth stating plainly. A clean instrument is not a sterile instrument. And for packaged steam-sterilized surgical instruments, do not rinse after sterilization — doing so would compromise the sterile state the process just achieved. Some liquid chemical sterilization systems are an exception and include a validated rinse as part of the cycle; follow that system’s own instructions. Sterilization parameters themselves come from the instrument IFU, the sterilizer IFU and your facility’s validated cycles, which is why no temperature or cycle time is given in this guide.

Medical Instrument Cleaning vs Medical Equipment Cleaning

This guide covers reusable hand-held medical and surgical instruments. Larger powered or electronic medical equipment follows different procedures and its own manufacturer instructions.

The practical difference is immersion. Hand instruments are generally immersible and are cleaned, rinsed, dried, inspected and then processed further. Powered equipment, electrical units and devices with electronic components, optics, seals or non-immersible parts often cannot be immersed at all and are cleaned by wiping with a compatible product.

Where a device combines both — a powered handpiece with detachable instruments, for example — each part follows its own instructions. Do not apply a hand-instrument method by analogy to equipment that was never designed for it.

Common Instrument Cleaning Mistakes

Most cleaning failures come from a small number of repeated mistakes, and nearly all of them happen before an instrument ever reaches the sterilizer.

• Letting soil dry. Dried soil is substantially harder to remove and compromises everything downstream. This starts at the point of use, not in the decontamination area.
• Using hot water for the first rinse. Heat coagulates blood proteins onto the surface, effectively baking on the soil you are trying to remove. Start cool.
• Using the wrong chemistry. Household products, incompatible chemistries and incorrect dilution cause staining, pitting and corrosion that cannot be reversed.
• Cleaning instruments closed. A hinged instrument cleaned in the locked position leaves soil in exactly the place inspection is hardest.
• Using a lumen brush of the wrong diameter. An undersized brush passes through without touching the channel wall and cleans nothing.
• Assuming ultrasonic suitability. Some materials, coatings and assemblies should never be processed ultrasonically.
• Overloading trays and stacking instruments. Solution and spray cannot reach surfaces that are covered by other instruments.
• Reusing soiled cleaning solution. As solution accumulates organic material its cleaning power drops and it can redeposit soil.
• Rushing rinsing and drying. Residual chemistry and trapped moisture cause staining and corrosion, and wet instruments cannot be inspected properly.
• Skipping inspection. Without it, a dirty or damaged instrument moves into a set and is discovered during a procedure.

Frequently Asked Questions

What is the best cleaning solution for medical instruments?

There is no single best solution. Neutral or near-neutral pH detergents formulated for instrument reprocessing are the most widely used because they combine good soil removal with strong material compatibility, and enzymatic formulations help with organic soil. The correct choice depends on the instrument material, the soil and what the instrument IFU permits. Household products are not suitable.

What chemical is used to clean surgical instruments?

Detergents and enzymatic cleaning products made specifically for medical device reprocessing. Enzymatic formulations typically contain proteases for blood and tissue, and may include lipases for fats and amylases for starches. Alkaline-based agents are also used but carry a higher corrosion risk. The concentration, temperature and contact time come from the chemistry manufacturer and your validated procedure.

How do you clean surgical instruments before sterilization?

Prevent soil from drying at the point of use, transport the instruments to the decontamination area in a closed container, open or disassemble them as the IFU directs, rinse in cool water, clean using the permitted manual or mechanical method, rinse away all chemistry and soil, dry completely and inspect before packaging. Exact parameters come from the IFU and facility procedure.

Can you clean surgical instruments with bleach, hydrogen peroxide or vinegar?

No. Bleach and other chlorine-containing products cause pitting and corrosion in stainless steel. Vinegar and other acidic products attack the passive surface layer that protects the metal. Household hydrogen peroxide is not a cleaning agent for instruments, although some peroxide-based formulations are made for device processing. None of these removes soil the way a purpose-made instrument detergent does, and damage from them is permanent.

Can medical instruments be cleaned in an ultrasonic cleaner?

Many can, particularly devices with fine serrations, box locks or difficult-to-reach features. But not every device or material is compatible — some coatings, dissimilar-metal assemblies and most powered or electronic devices should not be processed this way. Confirm compatibility in the instrument IFU and follow the ultrasonic unit’s instructions for solution, loading and cycle time.

What is the proper procedure for cleaning medical equipment?

Larger powered and electronic medical equipment is usually cleaned by wiping with a compatible product rather than by immersion, and follows its own manufacturer instructions. The immersion-based process described in this guide applies to reusable hand-held instruments, not to monitors, powered units or devices with electronic components.

Does cleaning sterilize medical instruments?

No. Cleaning physically removes soil, which is a requirement before sterilization can work, but it does not make an instrument sterile. Sterilization is a separate validated process carried out after cleaning, drying, inspection and packaging.

Should surgical instruments be rinsed after sterilization?

For packaged steam-sterilized surgical instruments, no. Rinsing belongs to the cleaning stage, before sterilization, and rinsing a sterilized package would compromise the sterile state. Some liquid chemical sterilization systems are an exception, with a validated rinse built into the cycle — follow that system’s instructions.

Medical Instruments and Reprocessing Accessories

Instruments that are cleaned, inspected and stored properly stay usable for years. Explore the full range of Peak Surgicals medical instruments, or browse surgical instruments, sterilization baskets and sterilization cassettes and trays for organising instruments through cleaning and reprocessing.

For a visual guide to instrument families, see medical instrument names, pictures and uses.

Unless stated on the individual product page, Peak Surgicals instruments are supplied non-sterile and must be cleaned, inspected and processed according to the applicable manufacturer IFU and the facility’s validated protocols before clinical use.