How to clean and disinfect your microscope

Germs spread easily so keep yourself, your co-workers and your family safe with good microscope sanitation.

Just as you wash your hands before meals, you should routinely clean and disinfect your microscope to prevent the spread of infection – and to keep your equipment in good working order. This is particularly important in shared work or school environments.

Here are some steps for keeping your microscope in good shape while keeping contamination to a minimum.

Glove up

You’ll need:

  • Soap and water or hand sanitiser
  • Disposable gloves

Priority one is to protect yourself when you’re cleaning the equipment. Wash your hands well (or use hand sanitiser), then don a pair of disposable gloves. This prevents you from accidentally contaminating the microscope and helps ensure you don’t touch any infectious microorganisms while you’re cleaning.

Clean the frame

You’ll need:

  • 2 clean cloths
  • Detergent/soap
  • Water or distilled water

Before you can properly disinfect your microscope, you need to first remove any dust or dirt that could be hiding dangerous microorganisms.

  1. Remove any dust by wiping the microscope down with a clean (dry) cloth. Work from top to bottom to prevent any stray dust or dirt falling onto areas you’ve already cleaned.
  1. Clean the microscope body and non-lens parts using a cloth with a small amount of neutral detergent or warm soapy water. Pay particular attention to areas that see a lot of use – the focus knobs, eyepieces, nosepiece and stage handle.
  1. Wipe down the microscope with a damp cloth, preferably using lukewarm distilled water.

Disinfect the frame

Once you’ve cleaned your microscope, you’re ready to disinfect it.

You’ll need:

  • 70% ethanol solution
  • A clean cloth
  1. Wet or spray a clean cloth with the 70% ethanol solution.
  1. Wipe the microscope down with the damp cloth. As before, pay close attention to the areas that see a lot of use.

Clean and disinfect the lenses

It’s important to keep your optics clean and clear. Microscope lenses are easily scratched, and care should be taken to avoid damaging them.

You’ll need:

  • Lens paper
  • 70% ethanol solution
  • Air blower
  • Loupe or detachable microscope eyepiece (optional but recommended)
  1. Inspect your lenses using your loupe or eyepiece (looking down the opposite end to usual) to see how dusty or dirty your optics are. If you don’t have a loupe or eyepiece, just angle your head to catch the light reflecting off the lens – any dust or grime should show up.
  1. Use your air blower to get any loose dust and dirt off your lenses.
  1. Fold a piece of lens paper into a triangle so there is a point. (For larger lenses, you can also just fold the lens paper around one of your fingers to create a point.)
  1. Put a small amount of 70% ethanol onto the point of your lens paper.
  1. Starting from the centre, use the point of your lens paper to clean outwards in a spiral pattern until you reach the edge.
  1. As before, check the lenses for any remaining dirt, dust or discolouration. If necessary, repeat the cleaning process until the optics are clean and clear.


Be sure to safely dispose of your gloves, and to wash and sanitise your hands after you’re finished.


  • If using a can of compressed air as an air blower, avoid accidentally spraying your microscope with propellant – never shake the can, and give it a quick spray into the air before using it to clean out any condensation
  • Don’t use organic solvents such as paint thinner to clean your frame – it can damage your microscope.
  • Keep a dust cover on your microscope when not in use – it will help keep your microscope free of dust and airborne contaminants.
  • Remember to disinfect the rest of your workspace. Wipe down the whole area with a clean cloth then use 70% ethanol to reduce the risk of infection.
  • It’s important that you use only genuine lens paper when cleaning the optics – coarser materials can scratch and ruin the lens or the protective coating, and you’ll sadly find yourself in the market for a new one!
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