In this study the production of functional foods in terms of food safety in Estonia, Slovenia and Turkey were evaluated. The definition, classification and health benefits of functional foods were investigated. The legal aspects concerning functional foods were also considered. The probiotic yoghurt production was chosen as model production in this study. The properties of probiotic bacterial cultures, selection criteria and benefits of probiotic bacteria were given. The production steps for the probiotic yoghurt production in terms of food safety were also evaluated.