The viability of free and microencapsulation L. acidophilus La-5, L. casei - 01, L. helveticus LhB 02, B. bifidum Bb-12, K. lactis NRRL Y- 8279 and Sacch. cervisiae DSMZ 70449 cells in simulated gastrointestinal tract environment was determined. The viable cells of strains decreased significantly except B. bifidum and K. lactis in microencapsulated form as compared with their initial count in the presence of lysozyme (100 µg/ ml). The viability of all strains at pH 1.5 was less than that at pH 3.0 throughout exposure time (180 min). By increasing the concentration of bile salt, the resistance of all microorganisms decreased and there was a significant difference between their initial count and that after 180 min at 37ºC. Bile salt hydrolase (BSH) activity was detected with L. acidophilus and B. bifidum. The viability of all strains decreased with the increase of phenol concentration and exposure time. The release of viable cells from microcapsules in simulated colonic pH solution increased significantly as the exposure time increased from zero to 90 min at 37ºC.  Also strains were resistant to all antibiotics used in this study except yeast strains were susceptible to neomycin. Results of this study showed considerable difference in the percentage of hydrophobicity between strains. Generally the final number of viable cells of the strains was still above the levels suggested to produce their claimed health benefits. On the other hand the microencapsulation of strains protected them against adverse effects of GIT environment and enhanced their survivability.