Probiotic use as capable preventive and therapeutic strategy in different diseases varying from allergic to autoimmune disease has recently been reported. Three interacting factors including an aberrant intestinal microbiota, a 'leaky' intestinal mucosal barrier, and altered intestinal immune responsiveness have been suggested to be able to create a ''perfect environment'' for autoimmune disease development. Regulation of intestinal microflora composition by probiotics offers the possibility to influence the development of mucosal/systemic immunity besides autoimmune diseases. Although there is a large amount of conflicting data on the preventive/therapeutic effects of probiotics in ADs; there is fairly promising evidence to recommend as well. Thus, probiotic use cannot be generally recommended for primary prevention and therapy of ADs for now.