This document specifies the protocol for the verification of reference methods and validated alternative methods for implementation in the user laboratory. This document is applicable to the verification of methods used for the analysis (detection and/or quantification), confirmation and typing of microorganisms in: — products intended for human consumption; — products intended for animal feeding; — environmental samples in the area of food and feed production, handling; — samples from the primary production stage. This document is, in particular, applicable to bacteria and fungi. Some clauses can be applicable to other (micro)organisms or their metabolites, to be determined on a case-by-case basis. The technical protocols for the verification of validated qualitative methods and validated quantitative methods are described in Clauses 5 and 6. The technical protocol for the verification of validated alternative confirmation and typing methods is described in Clause 7. The protocols for the verification of non-validated reference methods are described in Annex F.