Aim Cloning of genes that differentially expressed in remodeling thoracic aorta of 2K1C hypertensive rats(2-kidney, 1-clip Goldblatt rats), which is important for understanding the molecular basis of hypertensive vascular remodeling. Methods We used suppression subtractive hybridization (SSH) to isolate differentially expressed EST in remodeling thoracic aorta. This led to identification of more than fifteen differential expressed sequence-tags(EST). After further cloned and sequenced and homology searched in Genbank with software Stand BLAST. Some differentially displayed genes coding protein were confirmed by western blot. Results We have obtained fifteen pieces of differentially displayed EST, such as cytochrome C and Bcl-2. Moreover, the results from Western Blot confirmed that cytochrome C is highly expressed in in remodeling thoracic aorta and Bcl-2 lowly expressed in remodeling thoracic aorta. Conclusion Cytochrome C is released from mitochondria in response to a variety of apoptotic stimuli, such as reactive oxygen radicals, calcium and ceramide. The Bcl-2 family of proteins serves as critical regulators of pathways involved in apoptosis. Bcl-2 protein is anti-apoptotic. Our data indicate that cell apoptotic mechanism may have important role in hypertensive vascular remodeling.