Cigarette smoke is a contributory factor for the cardiovascular disease, lung diseases and cancers as the dominant illnesses. The proteomic analysis of bovine aortic endothelial cells (BAECs) exposed to cigarette smoke has been performed in the broad (Non-linear pH 3-11) and narrow (Linear pH 4-7) range by using two-dimensional gel electrophoresis (2-DE). Out of an average 950 spots observed in 2-DE gels under pH 3-11, the expression level of 25 proteins significantly increased with an increase of cigarette smoke extract (CSE) level, whereas 21 proteins were strongly down-regulated. In narrow (4-7) pH range analysis, 80 proteins showed a significant change in expression level as compared with control. Some of the proteins were found to show similar spot intensity patterns in both the linear (4-7) and nonlinear (3-11) pH ranges. Most of the proteins identified in both pH conditions were found to be involved in apoptosis, inflammation, transcription modulator, signal transduction pathway, ROS production, cell proliferation and extracellular structure formation. In addition, extracellular structural proteins also responded to apoptotic signaling as an indicator. The findings of the present study can be used as an early biomarker to indicate the risks of cigarette smoke related diseases and also in the design of new therapeutic and diagnostic approaches to control these diseases.