Mutagenesis represents a powerful methodology for the analysis of protein structural and functional relationships and dissection of complex protein-protein interactions. The suicide substrate-like inhibitory mechanism of the proteins of the serpin superfamily offers unique challenges for the design of mutagenesis studies. All serpins share a well-characterized core structure and most adopt a metastable conformation that is required for inhibitory activity. Mutagenesis studies focused on the reactive center loop, the hinge region, protease-binding exo-sites, conformational stability, and accessory ligand binding domains have led to a well-established serpin inhibitory mechanism and have defined specific biological interactions and functions for a number of serpins in development, homeostasis, and host defense. Nonetheless, great care must be taken in the design and interpretation of serpin mutagenesis studies, since the rapid conformational changes that occur during serpin inhibition can be affected at many levels.