This study investigated the survival of free and microencapsulated probiotic bacteria in orange and apple juices. Eight different strains of probiotic bacteria were used in this study including Lactobacillus rhamnosus, Bifidobacterium longum, L. salivarius, L. plantarum, L. acidophilus, L. paracasei, B. lactis type Bi-04 and B. lactis type Bi-07. The free or microencapsulated probiotic bacteria were inoculated into orange and apple juices and their viability was assessed on a weekly basis for up to six weeks. oBrix, malic acid concentration, and pH were also monitored. Encapsulated probiotc bacteria survived in fruit juices throughout the six weeks of storage, whereas free probiotic bacteria lost their viability within five weeks. In general, fruit juices containing microencapsulated probiotic bacteria were more stable than those containing free probiotic organisms.