Probiotics are nutraceutical products which have been used substantially for supplementation of the intestinal microbiota. Probiotics have been indicated in the therapy of various disorders such as gastric ulcer, diarrhoea, gastroenteritis, inflammatory bowel disease, colon cancer, urogenital infection, allergy, respiratory infection and to promote the individual’s well-being. The present review article focuses on the mechanism followed by probiotics for inactivating the harmful antigens. The various microencapsulation techniques useful in improving the processing, transit and storage stability of probiotics have also been described. Microencapsulation process linked protection and increased survival rate of probiotics have been discussed systematically.