Weissella confusa 31, an isolate from human feces, possesses desirable properties as a probiotic strain, including bile salt resistance. W. confusa 31 is not inhibited by bile salts up to 0.3% concentration. Proteins affected by bile salts (0.05%) were examined by 2-D gel electrophoresis. Our proteomic analyses revealed that the intensities of 29 spots were changed, where 17 increased (including 2 spots observed only under the bile salts stress conditions) and 12 decreased. Proteins were identified by MALDI-TOF mass spectrometry. Proteins increased in the band intensities included adenylate kinase (12.75-fold increase), Clp-like ATP-dependent protease (11.91-fold), 6-phosphogluconate dehydrogenase (10.35-fold), and HSP 70 (5.07-fold). Some of the increased or decreased proteins are also known to be involved in other types of stress responses.