In brief
Pharmaceutical microbiology tests whether a medicinal product is free from viable microorganisms or whether its microbial load lies within the limits that apply to its use. For sterile products, this covers the sterility test, the bioburden before sterilisation and the detection of bacterial endotoxins. For non-sterile products, microbiological quality is determined, meaning how many microorganisms are present and whether specified pathogens are absent. Environmental monitoring of the cleanrooms is added to this.
A microbiological contract laboratory carries out these tests according to the methods of the European Pharmacopoeia (Ph. Eur.), demonstrates their suitability for your product and evaluates the results so that they can feed into batch certification. Because many tests take days to weeks, planning laboratory capacity is part of planning batch release.
When you need it
For sterile medicinal products, Annex 1 of the EU GMP Guide requires a sterility test of the finished product and a bioburden determination for every batch, both for aseptically filled and for terminally sterilised products. The data from environmental monitoring of the cleanrooms are taken into account when the batch is certified. Companies without their own microbiology department, or that need to absorb peaks, outsource these tests.
For non-sterile products such as tablets, ointments or oral solutions, the specification defines which microbial counts are acceptable and which pathogens must not be detectable. Active substances, excipients and pharmaceutical water are also tested microbiologically, depending on the specification.
Legal basis and rules
The test methods themselves are set out in the European Pharmacopoeia. How they are embedded in manufacturing is governed by the EU GMP Guide, and for sterile products above all by Annex 1, which has applied in full since 25 August 2024.
What is changing right now
The European Pharmacopoeia has abolished the rabbit pyrogen test. It was removed from the monographs with effect from 1 July 2025, and chapter 2.6.8 has been deleted since 1 January 2026. Since then, the manufacturer selects an in vitro test on the basis of a risk assessment. For endotoxin testing, the recombinant factor C method has been recognised as a separate chapter 2.6.32 since 1 January 2021. With edition 13.1 of the pharmacopoeia, it will be included on 1 January 2027 as one of seven methods in the revised chapter 2.6.14, and 2.6.32 will be deleted on the same date. Ask the laboratory to confirm which version it applies.
Requirements from Annex 1
Annex 1 stresses that the sterility test is only the last link in a chain of controls and cannot rescue a process that does not meet its requirements. The test must be validated for the product concerned, and the samples should represent the highest-risk parts of the batch, for aseptic filling for example containers from the beginning and the end. In environmental monitoring, any growth in cleanroom grade A must be investigated. Microorganisms from grades A and B must be identified to species level. Culture media for environmental monitoring and for media fills are tested for growth promotion before use, with a justified selection of reference strains and typical isolates from your own site. This test should normally be performed by the user, and outsourcing it must be justified.
How the collaboration works
What to look for when choosing a laboratory
Frequently asked questions
May the sterility test be performed externally? +
Do I still need the rabbit pyrogen test? +
Who defines environmental monitoring, we or the laboratory? +
What if the product’s shelf life is shorter than the duration of the sterility test? +
Sources
Every statement in this text was checked against these primary sources (as of 10.11.2026). Laws, guidelines and authority websites, no advertising.
- EU-Kommission (EudraLex) · eudralex-volume-4_en
- EU-Kommission (EudraLex) · 20220825_gmp-an1_en_0.pdf
- EU-Kommission (EudraLex) · 2014-11_vol4_chapter_6_0.pdf
- EDQM (Ph. Eur.) · ph.-eur.-bids-adieu-to-rabbit-pyrogen-test-in-its-monographs
- sukl.gov.cz · New-content-issue_12.1.pdf
- EDQM (Ph. Eur.) · ph.-eur.-allows-the-use-of-recombinant-factor-c-for-control…
- dmp.no · contents-of-the-ph.-eur.-13.1.pdf
- rssl.com · sterility-testing
- EDQM (Ph. Eur.) · european-pharmacopoeia
- EDQM (Ph. Eur.) · swan-song-for-general-animal-safety-tests-another-significa…
- EDQM (Ph. Eur.) · a-major-step-towards-animal-free-testing-for-the-test-for-b…
- EDQM (Ph. Eur.) · outcome-183-session-european-ph-commission
- ICH · Q4B Annex4A(R1
- ICH · Q4B Annex4B(R1
- ICH · Q4B Annex4C(R1
- ICH · Q4B Annex 14 Guideline.pdf
- sukl.gov.cz · Contents-of-Supplement_11-8.pdf
- ICH · Q4B Annex 8(R1
- mhlw.go.jp · 001372337.pdf