Microorganisms’ encapsulation refers to the principle of involving microbial cells with adequate wall materials to protect and control release. Probiotic microorganisms may be affected by extrinsic factors such as oxygen concentration, pH, temperature, etc. By definition, probiotics are bacteria or yeast, which when consumed in adequate quantities confer health benefits to the host. However, in order for beneficial effects to be achieved, microbial cells must stay viable in the colon. Therefore, encapsulation methods using hydrocolloids as wall material are reported as strategy for maintaining the probiotics viability against adverse conditions. The aim of this study was to evaluate the encapsulation efficiency and in vitro gastrointestinal survival of Lactobacillus reuteri ATCC 23272 encapsulated in alginate and alginate-carrageenan. The spheres obtained by the extrusion technique were constituted of alginate 15 g/L and alginate-carrageenan (15:2.5; 15:5; 15:10 g/L), containing approximately 9 log CFU/g of L. reuteri. Unencapsulated cells were used as a control in in vitro gastrointestinal survival tests. The addition of carrageenan to the spheres improved the encapsulation efficiency of L. reuteri, reaching rates greater than 96% (p≤0.05), while the sphere containing only alginate lost about 1 log CFU/g after extrusion. In in vitro gastrointestinal survival test, unencapsulated L. reuteri presented drastic reduce in the number of viable cells in 5.3 log CFU/mL, while alginate-encapsulated cells presented decrease of 2.2 log CFU/g. The protective effect of encapsulation against simulated gastrointestinal conditions was even greater (p≤0.05) using alginate-carrageenan (15:2.5 and 15:5 g/L) in the spheres composition, with a reduction of 1.2 log CFU/g after the test. This trend was expected, especially due to the porosity commonly found in alginate spheres, however the carrageenan may presented synergistic effect with alginate, improving the physical properties of the particles, consequently the encapsulation efficiency and protection of encapsulated cells under adverse conditions.