Disinfecting microscopes

Disinfecting Microscopes: I am looking for information to create a SOP (or something that Science assist can do for us?) for cleaning and disinfecting microscopes - what is the best and safest agent to use and how to keep a record of this within the prep room.  I am in particular wanting something that will be effective against enveloped viruses such as coronavirus.

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Publication Date: 21 May 2020
Asked By: Anonymous
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Disinfecting microscopes

Using microscopes during COVID-19

Shared equipment such as microscopes should be cleaned and disinfected between each use. If it is possible to allocate each student their own microscope in a lesson this will avoid the need for disinfecting during a lesson. Note that the use of safety glasses is not recommended, as they are not needed when using a microscope and they may introduce new risks such as additional face touching.

Here are some general guidelines formulated from the microscope manufacturer references noted below:


  • Disinfection will not destroy all microorganisms as it is not a sterilisation process. Disinfection will eliminate many microorganisms on inanimate surfaces and often requires certain exposure times. Common disinfectants are 70% ethanol, 0.5-1% bleach and 3% hydrogen peroxide1. It appears that most of the major microscope manufacturers recommend 70% ethanol to clean and disinfect their microscopes. Correlations with similar enveloped viruses to the emerging coronavirus indicates that 70% ethanol is effective.2
  • Caution is required as to the type of cleaning and disinfecting agent used as not all components of all microscope brands are able to withstand all disinfectants. There is the possibility of damage to the lenses and the cement used to hold them together. Generally, it is advised to use minimal cleaning or disinfecting solution. and never saturate the lens cleaning tissue. We recommend checking with the microscope manufacturer or user manual for the recommended disinfectant for your brand of microscope.
  • To avoid scratching the lenses do not use regular tissues, paper towel or cotton swabs for cleaning. Always use specific lens cleaning tissue.
  • It is recommended to wear gloves when cleaning and disinfecting the microscope. The gloves can be discarded into the regular bin after cleaning and hands should be washed with soap and water or sanitiser.

Body of microscope:

  • High touch areas of a microscope e.g. nosepiece, stage and slide holders and focus knobs should be wiped over with a soft cloth and mild detergent followed by a disinfectant.

Eyepiece (oculars) plus rubber eyepiece shades and objectives - cleaning and disinfecting.

  • It is recommended to initially blow any dust off with a blower brush. This is then followed by gentle cleaning and then disinfecting with 70% ethanol using lens tissue.
  • Remember to never saturate the lenses with cleaning or disinfecting solution, just lightly blot the surface then allow to air dry.

Note: It is not recommended to clean the internal surfaces of lenses.


An eyepiece microscope camera can be used to view images projected from the microscope onto a smart board. or computer screen.

Record Keeping

This is not mandated, however it is a good idea to keep records in a microscope maintenance log to demonstrate that disinfection has taken place. We don’t have a proforma for you to use, but you could make one up to suit your school circumstances, which would include as a minimum the date; microscope identification,  and which class (or student) used the microscope. It could also be used to identify where there is another issue with a specific microscope such as needing a replacement part (e.g. globe) or servicing (e.g. poor focusing or dirty lenses).

Good hygiene during COVID-19

Good hygiene should be strictly observed such as is stated in the Australian Health Protection Principal Committee (AHPPC) statements, see https://www.health.gov.au/committees-and-groups/australian-health-protec...

As the information is being frequently updated it is good to check the latest advice. As of (24th April 2020) the latest advice for schools can be found at https://www.health.gov.au/news/australian-health-protection-principal-co...

In particular, see the sections on hygiene, routine care and environmental cleaning. The general hygiene advice is 

  • Staff and students should stay away from school if unwell
  • Everyone should practice good hygiene: wash hands regularly, cough into elbows, minimise touching face
  • Clean and disinfect frequently used high touch surfaces and frequently used objects such as computers, photocopiers etc.

Manufacturer information for cleaning and disinfecting microscopes

Leica: ‘How to Sanitize a Microscope’, https://www.leica-microsystems.com/science-lab/how-to-sanitize-a-microsc...

Nikon: ‘Handling and Disinfecting Procedures for Nikon Microscope Products’, https://www.microscope.healthcare.nikon.com/en_AOM/recommended-handling-...

Olympus: ‘How to Clean and Sterilize Your Microscope’, https://miap.eu/fileadmin/primary/Public/user_uploads/Files/Ressources/O...

Zeiss: ‘Recommendations for Disinfection of Microscope Components and Objectives’, https://www.zeiss.com/content/dam/Microscopy/us/img/2019-Template/litera...

References and further reading

1 ‘How to Sanitize a Microscope’, Leica Microsystems website, https://www.leica-microsystems.com/science-lab/how-to-sanitize-a-microsc... (03 April 2020)

2 South Australian Health. March 2020. Fact Sheet for health professionals Coronavirus disease (COVID-19): environmental management, South Australia Health website, https://www.sahealth.sa.gov.au/wps/wcm/connect/58acb674-262e-4300-ac22-0... (Accessed via Coronavirus Disease 2019 (COVID-19) resources and links for health professionals, South Australia Health website, https://www.sahealth.sa.gov.au/wps/wcm/connect/public+content/sa+health+... )

‘Australian Health Protection Principal Committee (AHPPC)’ Australian Government Department of Health website, https://www.health.gov.au/committees-and-groups/australian-health-protec... (Accessed May 2020)

Science ASSIST. 2015. SOP: Use and care of the compound light microscope, Science ASSIST website, http://assist.asta.edu.au/resource/2879/sop-use-and-care-compound-light-...

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