Following a request from the European Commission in 2014, the EFSA Panel on Dietetic products, Nutrition and Allergies (NDA) was asked to provide scientific and technical guidance on foods for special medical purposes (FSMP) in the context of Article 3 of Regulation (EU) No 609/2013. The guidance presented in this document is to assist in the preparation and presentation of well-structured dossiers. It presents a common format for the organisation of the information and outlines the information and scientific data which could be included in the dossier, as well as the key issues which should be addressed in the dossier in order to assess the extent to which a food product notified as FSMP falls under the scope of Regulation (EU) No 609/2013, under the proposed use. It is intended that the guidance will be kept under review and will be further amended and updated as appropriate in the light of experience gained from the evaluation of dossiers for specific food products notified as FSMP, and in the light of future Community guidelines and legislation. The scope of this guidance is limited to FSMPs in the context of Article 3 of Regulation (EU) No 609/2013. Out of the scope of this guidance are: a) other categories of food falling under Regulation (EU) No 609/2013, such as infant formula and follow-on formula, processed cereal-based food and baby food, and total diet replacement for weight control; b) meal replacements for weight control; c) “gluten-free” and “lactose-free” foods. Upon request from the European Commission in 2020, this guidance has been revised to inform applicants of new provisions in the pre-submission phase and submission application procedure set out in Regulation (EC) No 178/2002, as amended by Regulation (EU) 2019/1381 on the transparency and sustainability of the EU risk assessment in the food chain, that are applicable to all applications submitted as of 27 March 2021.