The influence of microencapsulation in casein-based microcapsules produced by enzymatic gelation with transglutaminase on the viability of two probiotic strains, which differ in their sensitivity against dehydration, Lactobacillus F19 and Bifidobacterium Bb12 during freeze-drying and subsequent storage was investigated. Water activities after drying did not differ between free and encapsulated samples in all cases. However, Lactobacillus F19 survived in significantly higher numbers in the encapsulated state, compared to free cells (protein-cell-mixture). Storage conditions were varied in terms of relative humidity (11%/33%) and temperature (4 degrees C/25 degrees C). Encapsulation improved the survival of Bifidobacterium Bb12 during storage for up to 90 days under all tested conditions. Further co-encapsulation of prebiotic resistant starch corns negatively influenced the physical barrier of the protein matrix, hence leading to a reduction of the protective effect. In the case of Lactobacillus F19 no encapsulation-related protective effect was found during storage. (C) 2010 Elsevier Ltd. All rights reserved.