Probiotics are microorganisms that have a beneficial effect on the health of the host. However, before these effects can be referred to as beneficial to human health, such claims need to be evaluated by regulatory institutes such as the European Food Safety Authority (EFSA). The EFSA Panel on Dietetic Products, Nutrition and allergies (NDA) has published their opinions regarding health claims including probiotics, most of which were rejected in the past years. Using the EFSA database, the NDA dossiers published between 2005 and 2013 were analysed to provide an overview on what grounds certain health effects were accepted as beneficial and others not. The NDA Panel distinguishes between claims that are definitely beneficial, possibly beneficial or non-beneficial to human health. Overall, 78% of all analysed health claims are considered by the NDA Panel as (possibly) beneficial to human health, in particular the gut health effects. Since, in many cases, the scientific substantiation of a particular health claim was deemed insufficient, most applications were turned down. For future health claim applications concerning probiotics to be successful, they should include specific statements on what exactly the microorganism affects, and the scientific substantiation of the particular health claim should be based on the targeted (general) population.