This study characterizes the factors responsible for the cholesterol reduction by Lactobacillus acidophilus ATCC 43121. In addition, two-dimensional gel electrophoresis (2-DE) and protein profiling was also used to study the response of ATCC 43121 at the proteome level in the presence of cholesterol. The results show that the cell-free supernatant (CFS) produced by ATCC 43121 in the presence of bile salts could also reduce the cholesterol in the broth, whereas all previous reports have suggested a mechanism by live cells. The active fraction was partially purified by 60% ammonium sulfate precipitation, and subsequent Sephacryl S-100 column chromatography. The molecular weight of the component with cholesterol-reducing activity was estimated to be approximately 12 kDa by SDS-PAGE. These results suggest that the novel protein isolated from CFS may be an important factor in the mechanism for cholesterol reduction by ATCC 43121. In addition, the proteins expressed by ATCC 43121 in the presence of cholesterol micelles were detected by 2-DE, five protein spots with at least a 2.5-fold increase in amounts being identified. The responsible proteins may be involved in the stress-response, translation, and metabolic processes. These results may suggest a new possibility for the mechanism underlying cholesterol reduction by lactic acid bacteria (LAB), differing from the conclusions of previous reports.