Extracellular matrix (ECM) and ECM-hydrolytic enzymes play critical roles in reproduction, development, morphogenesis, wound healing, tissue repair, regeneration, and remodeling. They are also involved in pathological processes such as inflammation, arthritis, cardiovascular diseases, stroke, neurodegeneration, metabolic syndrome, and cancer invasion and metastasis. Other reviews summarized the structure and function of ECM-degrading enzymes in cancer and other diseases. This review will focus on current insights of major protease families and other digestive enzymes that play significant roles in ECM remodeling and ECM-related pathologies. For example, the functions of matrix metalloproteinases in modulating adipogenesis, and their subsequent implications in obese patients, are discussed. Recent discovery and characterization of nineteen members of the human disintegrin-metalloproteinase with thrombospondin motif family have revealed new opportunities of investigating these enzymes in human pathologies, especially in the pathogenesis of osteoarthritis. Although kallikrein-3 was discovered many years ago as prostate specific antigen, the biomarker for detecting human prostate cancer and monitoring its recurrence in patients after surgery, fifteen members of the kallikrein family were reported to participate in physiological and pathological processes. Furthermore, exciting research has been carried out on other important ECM-digestive enzymes, including heparanase, cathepsins, hyaluronidases, and matriptases. Research data have suggested that these enzymes are potential therapeutic targets and biomarkers for cancer, arthritis, obesity, diabetic complications, multiple sclerosis, cardiovascular diseases, cerebral vascular diseases, and many other pathological conditions.