Recent scientific evidence suggests the relevance of probiotics in the development and regulation of gut-associated lymphoid tissue (GALT). Probiotic strains perform regulatory activities by modulating the degree of immune activation in response to pathogens and tolerance toward food antigens. In addition, these flora can enhance effector T cell responses, making them ideal candidates for safe vaccine adjuvants, and they can also assist the humoral immune response by promoting amplified production of secretory IgA. The recent development of genetically modified bacterial strains characterized by co-expression of antigens and cytokines highlights the growing advancement of new therapeutic applications for probiotics that are specifically focused on GALT immune responses. In light of this innovation, recombinant probiotics could potentially be used in the future to prevent and/or cure food allergy, as well as reinduce oral tolerance to auto-antigens. Moreover, the immunological benefits of probiotic bacteria will most likely revolutionize the application of microorganisms in therapies for moderating adverse mucosal and systemic responses.