The definition of probiotics has evolved from a live active culture which improves the balance of the gut microbiota composition to specific effects, in particular, the immunomodulatory potential of clearly defined strains. The strains with beneficial properties, potential sources of probiotics, most frequently belong to the genera Bifidobacterium and Lactobacillus, and some of these strains exhibit powerful anti-inflammatory properties. Indeed, probiotic therapy has attracted research interest in human infectious, inflammatory and allergic disease. The most fully documented disease altering the gut microbiota is acute infectious diarrhoea in childhood. Current probiotic research aims to provide safe but sufficient bacterial stimulus in order to avert deviant immune responsiveness related to allergic and inflammatory diseases. However, further rigorous scientific efforts are required to characterize the immunomodulatory potential of specific probiotic strains for these targets.