This working document has been prepared to address the assessment of secondary metabolites of microbial biocontrol agents. The main focus of this working document is the assessment of the hazards and risk of secondary metabolites produced during the manufacturing of microbial pest control products and after their application in the field. This document addresses a number of important topics for secondary metabolites, including concerns that microbial pest control products could be associated with known or as yet uncharacterised ‘new’ secondary metabolites. A background document is available as an annex to help provide clarity on issues and terminology related to secondary metabolites of microbial biocontrol agents. This document may also form the basis of a future OECD Guidance Document on the subject.