The effect of microencapsulation on the viability of Lactobacillus casei, L. paracasei, L. acidophilus Ki and Bifidobacterium animalis BB-12 during exposure to lethal conditions (25% NaCl, pH 3.0 and 55–60 °C) was evaluated. Results demonstrated that survival of probiotic strains to the imposed lethal stress conditions was strain dependent. With the exception of exposure to 25% (w/v) NaCl, L. acidophilus Ki (free and encapsulated cells) demonstrated the highest survival rates through exposure to lethal conditions of temperature and pH. For this probiotic strain exposed to heat, microencapsulated cells expressed a higher heat tolerance at 55 °C than free cells. For the other tested bacteria, in general, encapsulation had no positive effect on survival through the tested lethal conditions.