Probiotic bacterial encapsulation systems have proven useful in protecting the bacteria from gastric acids, bile salts and other drastic conditions present in the gastrointestinal tract. In addition, daily intake of probiotic products has shown positive therapeutic effects on gastrointestinal and autoimmunity problems. Polysaccharides have aroused great interest in probiotic food applications due to their non-toxicity, biocompatibility, and the fact that they can be digested by enzymes in the gastrointestinal tract. The proper selection of an encapsulation system through the adequate combination of matrices and methods shows increased viability and provides a very promising shield for probiotic against various stress factors during processing, digestion, and storage conditions. Although most research has been conducted on simulated digestion, it is suggested to undertake systematic in vivo investigations of encapsulation efficacy where both the method and the encapsulation system are studied. The focus of this review is to provide an overview of the evolution of traditional encapsulation methods and the use of polysaccharides as efficient encapsulation systems. A second topic briefly reviewed are trends in encapsulation strategies and microencapsulation systems for non-dairy probiotic products. Finally, a new generation of probiotics as a preventive and therapeutic tool for different diseases, is showed.