Background: Various decellularization methods have been studied in order to develop tissue graft which is less immunogenic and more durable. This study was performed to investigate the physico-dynamic and histological effect of trypsin pretreatment on decellularization protocols. Material and Method: Two groups of bovine pericardium specimen each underwent decellularization process based on SDS and Triton X-100 or N-lauroylsarcosinate and Triton X-100. Two more groups additionally underwent pretreatment with 0.1% Trypsin/0.1% EDTA. After decellularization process, mechanical tensile strength was tested, then biomechanical test of permeability and compliance was tested before and after fatigue test. Light microscopy and electron microscopy was performed to observe histological findings. Result: There was no difference in mechanical tensile strength between groups, but permeability and compliance was decreased in trypsin pretreated groups. Light microscopic and electron microscopic findings revealed damage of the extracellular matrix in trypsin pretreated groups and in groups which underwent the fatigue test also. Conclusion: Trypsin pretreatment in decellularizing process of bovine pericardium damages extracellular matrix and increases permeability and compliance of the bovine pericardium, but did not decrease tensile strength. Further studies are needed to use enzymatic treatments in decellularization protocols.