This article reviews pertinent legislation regulating the safety of probiotics within the European Union (EU). Currently available probiotic organisms and known issues regarding their safety are briefly summarised. While most of the species and genera, particularly lactobacilli and bifidobacteria are apparently safe, certain micro-organisms may be problematic; particularly the enterococci, which are associated with nosocomial infections and harbour transmissible antibiotic resistance determinants. At present, probiotic human foods are not governed under specific EU regulatory frameworks, although the Novel Food Regulation EU 258 / 97, could be relevant in some specific cases. However, microbial feed additives (regulated by Council Directive 70 / 254 / EEC and in accordance with guidelines of the Scientific Committee on Animal Nutrition (SCAN)) are subjected to detailed safety assessment with the intention of ensuring that they are innocuous to target animals, users and consumers. Particular attention is focused on the presence of transmissible antibiotic resistance markers, and to the potential for production of harmful metabolites. The guidelines do not differentiate between species and strains with long histories of safe use and other micro-organisms. This has caused some concern regarding overregulation, if the same principles are to be applied to probiotics or starter cultures intended for human food use. Accordingly, SCAN has launched an initiative towards a “Qualified Perception of Safety” (QPS) concept, which would allow strains with established safety status to enter the market without extensive testing requirements. It is likely that the European Food Safety Authority (EFSA) will play a central role in the regulation of both human and animal probiotics.