Bacterial species that have traditionally been regarded as safe are used in probiotics; the main strains used include lactic acid bacteria and bifidobacteria that inhabit the intestinal tracts of humans and animals. However, reports of frequent isolation of bacteria used in probiotics from infection sources in recent years have raised much debate over the safety of probiotics. This article describes the status quo of isolation of probiotic bacteria from infections and reviews each of the factors that have to be addressed in assessing the safety of probiotics, namely pathogenicity, infectivity, toxicity, and intrinsic properties of the bacteria. Monoassociation with Bifidobacterium longum in gnotobiotic mice as a method to assess safety with respect to infection, and translocation and immune responses as a result of the monoassociation are also described.