Beneficial microbes enter the food supply primarily through fermented foods (largely milks) and addition of probiotics. Fermented milks are a significant component of the diet of some geographical regions, including Europe. The fermentation process serves to preserve safety, nutritional quality and palatability of milk. In addition, the microbes associated with fermented milks and probiotics are associated with human health benefits. However, in the area of health claims only one claim for beneficial microbes has been approved in the European Union, that is for yoghurt to improve lactose tolerance. We searched for health messages that include probiotics or fermented milks in nutrition guidelines and recommendations in thirteen countries of the EU plus Switzerland. Such messages are allowed when they are made by non-commercial government bodies. Our analysis revealed that five EU member states have national nutrition guidelines or recommendations that include either probiotics or fermented milks with live bacteria. This supports that some EU member states recognise health benefits associated with consumption of live microbes, even if commercial marketing claims are not authorised. Harmonisation between recommendations and approved health-claims would benefit consumers and public health.