Degeneration processes that affect bioprosthetic heart valves made from glutaraldehyde treated bovine pericardium are poorly understood. The present study undertook the identification and characterization of matrix metalloproteinases (MMPs) in extracts obtained from 28 pericardial derived bioprosthetic heart valves explanted at surgery. A lysosomal marker was used to assess the incidence of infiltrating extracellular matrix degrading cells. The major biochemical features that were associated with tissue degeneration and bioprosthetic heart valve failure were increased levels of MMP 9, high levels of beta-glucuronidase, and constant levels of active collagenase and MMP 2. The MMPs extracted from ruptured bioprostheses were inhibited by calcium chelators and zinc binding compounds. These data suggest that tissue failure, in addition to known mechanical and calcification related factors, may be contributed to by the intervention of proteolytic enzymes. A schematic working model was proposed that described the major biochemical pathways underlying tissue degeneration, starting from bioprostheses preparation and ending with clinical failure.