This review, which has been prepared within the frame of the European Union (EU)-funded project MARLON, surveys the organisation and characteristics of specific livestock and feed production chains (conventional, organic, GM-free) within the EU, with an emphasis on controls, regulations, traceability, and common production practices. Furthermore, an overview of the origin of animal feed used in the EU as well as an examination of the use of genetically modified organisms (GMOs) in feed is provided. From the data, it shows that livestock is traceable at the herd or individual level, depending on the species. Husbandry practices can vary widely according to geography and animal species, whilst controls and checks are in place for notifiable diseases and general health symptoms (such as mortality, disease, productive performance). For feeds, it would be possible only to make coarse estimates, at best, for the amount of GM feed ingredients that an animal is exposed to. Labeling requirements are apparently correctly followed. Provided that confounding factors are taken into account, practices such as organic agriculture that explicitly involve the use of non-GM feeds could be used for comparison to those involving the use of GM feed.