A wide range of human diseases are associated with the aberrant activity of mammalian, viral, bacterial or parasitic proteases. These include members of all four classes of proteases, namely, serine, cysteine, aspartic and metallo- proteases. The involvement of proteases in disease states has provided the impetus behind studies related to the design of potent and selective inhibitors and their use as either therapeutic agents and/or pharmacological probes to gain a better understanding of the pathophysiology of a particular disease. This review focuses on recent developments related to the design of mechanism-based and alternate substrate inhibitors of serine proteases of mammalian and non-mammalian origin. Numerous examples are cited that illustrate the fundamental principles and subtleties associated with the design of covalent and non-covalent inhibitors of these enzymes. This is an exciting and promising area of investigation that will undoubtedly continue unabated in the future.