The main requirement in the selection of probiotic strains is their survival in the gastrointestinal tract and to achieve the effect of probiotic need to ingest a high number of live probiotic bacteria in concentrated, powdered preparation that can be obtained by lyophilisation. Therefore, this study examined the survival of probiotic bacteria Lactobacillus helveticus M92, L. plantarum L4 and Enterococcus faecium L3 during freeze-drying with the addition of various lyoprotectors: sucrose, lactose, inulin, sorbitol and skim milk. The best survival of probiotic strains L. helveticus M92 and L. plantarum L4 was obtained in the presence of skim milk and inulin, and E. faecium L3strain in the presence of lactose, sorbitol and skim milk. Indigenous isolates of LAB, selected on the basis on in vitro simulated gastrointestinal tract conditions test, survive freeze-drying process in greater numbers when they are present lyoprotector skim milk or inulin. Isolate BGLE1-6 survives better in the presence of inulin, while isolates BGAL1-1-17 and ZG3 better survive freeze-drying process in skimmed milk powder. Microincapsulation in alginate, κ-carrageenan and casein action of transglutaminase, have been successfully applied to all three probiotic strains: L. helveticus M92, L. plantarum L4 and E. faecium L3. Microincapsulation maximum efficiency in all three cerriers is achieved by the probiotic strain L. helveticus M92. Lyophilisation of selected strains of LAB with different lyoprotectors and translation microincapsulation three selected carriers contribute to increasing the number of living bacterial cells in probiotic products as well as during exposure to adverse conditions of the gastrointestinal tract which contribute to the expression of their probiotic effect when they are implemented as bioterapeutics.