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Research on prostheses for repairing abdominal wall defects has progressed through past decades for developing an ideal prosthesis. The study was designed to compare different extracellular matrix (ECM) derived biological prostheses as alternate to conventional synthetic polymeric prostheses for the repair of full thickness abdominal wall defects. Five biological scaffolds derived from bovine diaphragm, bovine aorta, bovine gall bladder, porcine gall bladder, and rabbit skin were prepared and screened for their in vitro biocompatibility. Decellularized ECMs were subjected to various biocompatibility analyses, namely, water absorption potential, matrix degradation analysis, biomechanical testing, and cytocompatibility analysis. Though the rabbit skin displayed maximum biomechanical strength, due to its rapid degradation, it failed to fulfill the criteria of an ideal prosthesis. ECMs derived from bovine diaphragm and aorta were found to be superior than others based upon hydration and matrix degradation analysis, with best scores for bovine diaphragm followed by bovine aorta. The bovine diaphragm and aorta also displayed sufficient biomechanical strength, with diaphragm being the second highest (next to rabbit skin), in biomechanical strength followed by aorta. None of the biological prosthesis revealed any cytotoxicity. Thus, bovine diaphragm and aorta derived ECM fulfill the necessary criteria for their use as biological prosthesis. Because these prostheses are biocompatible, apart from their low cost, ease of availability, and simple preparation, they present a potential alternative to synthetic prosthesis for repair of abdominal wall defects, especially in veterinary patients.