The ability of microorganisms to synthesize S-layer, the outermost structure of the microbial cell envelope composed of non-covalently bound proteins, has been ascribed to help microorganisms to exert their probiotic properties in the host. In this work, formation of S-layer by the potentially probiotic strain Lactobacillus acidophilus IBB 801 under different stress culture conditions (high incubation temperatures, presence of bile salts or NaCl, and acidic pH) was assayed. A marked S-layer synthesis by L. acidophilus IBB 801 was detected when the strain was grown at 42°C and in the presence of 0.05% bile salts or 2.0% NaCl. The presence of S-layer proteins was further confirmed by transmission electron microscopy and protein identification by MS/MS. The differential expression of the proteome of this strain at 42°C, when a marked formation of S-layer was detected, revealed the overexpression of six proteins mainly related to general stress and protein biosynthesis and translation, while four proteins detected in lower amounts were involved in DNA repair and energy metabolism. As L. acidophilus IBB 801 produces both a bacteriocin and S-layer proteins, the strain could be of interest to be used in the formulation of functional food products with specific properties.