How to Clean Your Microscope

How to clean your microscope

What you’re doing is important and a clean microscope is key to quality images and longer lasting equipment. Regular cleaning also decreases your risk of infection from germs, which can remain on surfaces like metal, glass and plastic for hours or days. 

These simple steps show you how to keep your microscope clean and sanitised – for everybody’s safety.      

Materials needed

  • Disposable gloves
  • At least two clean, soft cloths
  • Lens paper
  • Air blower for optical lenses
  • 70% ethanol solution in a spray bottle
  • Soap and access to running water or hand sanitiser


  • Wear gloves – there’s no point in a clean microscope if you infect yourself in the process.
  • Discard gloves after each cleaning and use a different set of gloves for disinfecting.
  • After you finish disinfecting your device, discard the gloves and wash your hands thoroughly with soap and water.


Microscope Optics Cleaning Kit

Cleaning the microscope frame

Pay particular attention to the user ‘contact points’. These are the eyepieces, focus knobs and frame – plus your computer keyboard and mouse, if you are using them at the same time.

  1. Use a clean, dry cloth to wipe visible dirt – dust and other particles – off the frame. Start at the top and work towards the floor. This helps prevent particles from falling on parts of the microscope you have already cleaned.
  2. Wipe the surface in one direction. Wiping in a back and forth motion can create more particles.
  3. Make sure to use a different section of the clean cloth each time to avoid reintroducing particles.
  4. Use lukewarm water and a cloth to remove any stubborn dirt or stains off knobs, handles, eyepieces or the nosepiece in particular. These are commonly touched during microscope operation, so they must be cleaned and sterilised carefully. Avoid touching any lenses.
  5. Disinfect the frame and components with 70% ethanol. This will sterilise the equipment without damaging it. Try to avoid using other organic solvents as they can damage plastic components. Higher concentrations of ethanol can also dehydrate microorganisms rather than kill them.

Note: You’ll need a higher quality disinfectant if you work with more hardy or virulent organisms.

Cleaning the microscope optics

Your microscope’s performance relies on contaminant-free optics – lenses, filters and prisms.

  1. Check your lenses for dust using your eyepiece, or a jewellers loupe if you have one.
  2. Use an air blower to gently remove any visible dirt or dust.
  3. Then take a lens paper folded into a point and dampened with 70% ethanol to disinfect the surface. Be sure to use genuine lens paper because other products can scratch the lens.
  4. Starting from the centre of the lens, wipe in a circular motion and work outwards. Discard the lens paper after each use.
  5. To clean the surfaces of the condenser, hold a piece of lens paper between your middle and index fingers, then fold and wrap it around your index finger. Hold the tissue down with your thumb while wiping the lens surfaces clean.
  6. Check for any residual dirt or dust with your eyepiece or loupe. If any remains, or if the lens reflection looks uneven, repeat the procedure again, always using clean lens paper.
  7. Reattach your cleaned components

Keeping your microscope in great shape will help protect your investment for years to come.

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