To better understand the natural killer (NK) cell cytotoxicity mechanism at the proteome level, we comparatively analyzed the proteome of the human NK-92 cells which participate in NK cell-mediated cytotoxicity assay and that of control cells. Soluble proteins were separated by two-dimensional gel electrophoresis (2-DE), 75 protein spots were found to be reproducibly differentially expressed between control and cytotoxic human NK-92 cells. A total of 60 different proteins were unequivocally identified by MALDI-TOF MS coupled with database interrogation; 37 proteins were up-regulated, whereas 23 proteins were down-regulated. Western blotting analysis of heat shock protein 60 (HSP60) and cathepsin W verified their proteome results. Some of identified proteins are involved in NK-92 cytotoxicity, which is consistent with the literature. In addition, we modeled the pathway networks between differentially expressed proteins and cellular processes of secretion and exocytosis through PathwayStudio software. The results of this study help to provide insight into the molecular mechanism of NK cell cytotoxicity.