Allergic disease has been a global problem for the past few decades. Allergic diseases have a generally significant impact on the healthcare system and society and are considered to be one of the most common causes of chronic illness and hospitalization. The functional ability of probiotics to modulate the innate/acquired immune system results in the initiation of mucosal/systemic immune responses. The gut microbiota plays beneficial roles in food digestion, immune system development, control/growth of intestinal epithelial cells and their differentiation. Taking probiotics results in significant changes in gut microbiota and modulates cytokine secretion, including increased gene networks, TLRs, signaling molecules, and gut IgA responses. The regulation of the Th1/Th2 balance is done by probiotics, which inhibit the Th2 response and switch to Th1, thereby preventing allergies.