Accreditation, as the formal recognition of a laboratory's competence, is increasingly important in the field of plant pathogen diagnostics. As it is necessary to consider the scope of accreditation this paper presents the main differences between the fixed and flexible scope of accreditation and discusses the applicability of the flexible scope to plant pathogen diagnostics. This assessment is supported by practical experience gained during the testing of genetically modified organisms (GMOs) according to standard ISO/IEC 17025, starting with the fixed scope in 2003 and proceeding to the partially flexible scope in 2006. With increasing flexibility, more responsibility is transferred to the laboratory during this process and procedures governing validations need to be clearly specified. Our processes of planning, performing, documenting, and evaluating results of in‐house method validations are general and applicable to the validation of different methods. They are presented here with the example of real‐time PCR validation, a method that is increasingly used in plant pathogen diagnostics due to its reliability and high sensitivity.