BACKGROUND: It has been found that xenogenic extracellular matrix (ECM) may cause a strong inflammatory response in humans during clinical application of decellularized porcine heart valve (synergraft valves). An early inflammatory reaction severely weakens matrix structure of valve wall, leading to structural rupture and decay of grafts. From Synergraft's event, the decellularized porcine heart valves still had immunogenicity, especially for pediatric patients. The mechanisms by which the ECM triggers this immune process need to be further evaluated. OBJECTIVE: To find the difference of gene sequence between human and porcine ECM and to identify the ECM immunogenicity based on bioinformatics. DESIGN, TIME AND SETTING: A contrast study between human and porcine ECM based on type IV collagen was performed at the Laboratory of Cardiothoracic Surgery, Changhai Hospital, the Second Military Medical University of Chinese PLA from June 2008 to February May.MATERIALS: The fresh porcine heart valves were obtained from Shanghai Wufengshangshi Slaughter House. Decellularized porcine aortic valves, hybridoma cells, and monoclonal antibodies were provided by our laboratory. METHODS: Similar region and conservative site of gene sequence among human, porcine, and rat were compared so as to look for common similar region, site, and sequence difference and investigate the segment which caused common and different gene sequence. Type IV collagen monoclonal antibody was used to evaluate the persistence of ECM of decellularized porcine heart valve following immunohistochemical staining. MAIN OUTCOME MEASURES: Type IV collagen gene sequence; efficacy of self-made antibody using immunohistochemistry; effect of self-made antibody on type IV collage of decellularized porcine heart valve. RESULTS: The differential gene serial in type IV collagen protein was found out by bioinformatics method. Monoclonal antibodies were successfully produced by human-mouse hybridoma technique. Residual porcine ECM was observed on decellularized porcine heart valve. CONCLUSION: Residual porcine ECM was observed on decellularized porcine heart valve and had immunogenicity.