Microorganisms have a long history of use in food production, e.g. in the production of sausages, cheeses, etc. Roughly one quarter of all food products rely on microbiological processes, and the safe use of microorganisms for food production is essential. The transfer of novel traits to food microorganisms through recombinant gene technology will result in new potential food safety issues. This requires the elaboration of criteria for safety assessment of foods derived from genetic microorganisms. This joint FAO/WHO Expert Consultation was convened to consider criteria for the safety and risk assessment of food and food ingredients produced with the aid of, or containing, viable or non-viable genetically modified microorganisms (GMMs). The outcome is meant to contribute to safety and regulatory considerations by Member States and to support the development of international safety assessment guidelines for food produced with the aid of GMMs (GMM food) by the Codex ad hoc Intergovernmental Task Force on Foods Derived from Biotechnology. The Consultation concluded that the safety and risk assessment of GMM foods should proceed on a case-by-case basis considering both safety and nutritional aspects. The assessment should use the concept of substantial equivalence as a starting point, identifying differences and similarities between GMM foods and their conventional counterpart. While these differences guide the assessment, a number of additional issues require special consideration. Examples are the potential persistence of the GMM in the host gut and its interaction with the endogenous microflora, including the transfer of new genes to the gut microflora. Likewise the interaction of new genetic material with human cells in the gut, including the immune system, should be considered. The assessment of GMM foods take into consideration the history of safe use of microorganisms used in the construction. The genetic stability and pathogenic potential of the strains, as well as possible secondary effects of the genetic modification on metabolism, including the concentration of critical nutrients, antinutrients, etc. are important factors to consider. Antibiotic resistance marker genes should be avoided and their absence from the final GMM food ensured. In order to provide the basis for improved safety and risk assessment of GMM food, the Consultation recommends strengthening the capability to analyze the complex ecosystem in the human gastrointestinal tract, including work on colonization, persistence, gene transfer and host interactions. New technologies, such as molecular profiling, are developing rapidly with a potential to enhance the assessment of GMMs. The Consultation encourages further development and validation of such methods. Fermentation provides a simple technology used globally to produce food of high nutritional and hygienic quality; a technology, which is especially important in developing countries. The Consultation recommends capacity-building efforts to support the needs of developing countries in improving and evaluating this technology and its potential also in relation to GMM use. To enable efficient interaction and transparency in the safety and risk assessment of GMM food, FAO and WHO is urged to coordinate efforts to enhance the communication of safety and risk assessment principles of GMM food to all stakeholders including the public.