Genetically modified microorganisms (GMMs) are involved in the production of a variety of food and feed. The marketing of these products within the European Union falls under different legislative instruments, which establish the requirement for a risk assessment for the authorisation of the product. The present guidance describes the principles to be followed when conducting such a risk assessment, as well as the scientific information required in applications for authorisation to be evaluated by the Scientific Panel on Genetically Modified Organisms of the European Food Safety Authority (EFSA GMO Panel). Products form four categories, depending on their nature and the level of scientific information required for their evaluation by the EFSA GMO Panel. The guidance details the data to be provided for the assessment of products of each category, providing reference to other guidance that is also applicable. This document draws on the experience gained by the EFSA GMO Panel in assessing applications for marketing food and feed involving GMMs and takes into account the input received from different stakeholders, and updates the “Guidance Document for the risk assessment of genetically modified microorganisms and their derived products intended for food and feed”, adopted by the EFSA GMO Panel in 2006.