Organisms have evolved to react to stress, tissue damage and pathogen invasion to assure their survival. Leukocytes are the primary responders and they regulate repair, immune defense and inflammation with the aid of a wide variety of other cells (e.g. epithelial, fibroblasts). To assure proper responses, a plethora of proteins are involved including signaling molecules, chemokines and proteases to orchestrate a step-by-step reaction. Inflammation is an essential biological process, however, when it persists, it can lead to various diseases that are challenging to heal or cure. The technologies and techniques covered in this book chapter can be applied to study all proteases and their inhibitors although will be centered on the matrix metalloproteinases (MMPs). It will focus on the proteolysis performed by MMPs, their various beneficial and detrimental effects in inflammation and the novel methods to study their roles on human diseases.