We employed rat pheochromocytoma PC12 cells as our model system to identify cellular proteins that accompany Escherichia coli lipopolysaccharide (LPS)-induced apoptosis, based on a proteomic approach. Cell viability tests revealed that naïve PC12 cells underwent cell death in a dose-dependent manner after treatment with LPS. Flow cytometric analysis confirmed that apoptosis was primarily responsible for the observed cell death. Two-dimensional electrophoresis in conjunction with N-terminal sequencing, immunoblot, matrix-assisted laser desorption/ionization-time of flight analysis or computer matching with protein databases further revealed that the LPS-induced apoptosis is accompanied by an augmented level of calreticulin, calcium binding protein 50, endoplasmic reticulum protein 60 (ERP60), heat shock protein 60 (HSP60) or HSP90, and a reduced level of amphoterin, cytochrome c oxidase polypeptide VIa-liver or ERP29. These proteins are associated with endoplasmic reticulum, mitochondria or cell membrane, and are with known or potential roles in apoptosis. Their identification therefore provides an impetus for further delineation of the cellular and molecular basis of apoptotic cell death and sepsis based on proteomic profiling of PC12 cells.