Carbohydrate antigens are immune targets associated with a variety of pathogens and tumor cells. Unfortunately, most carbohydrates are intrinsically T cell-independent antigens, which diminishes their efficacy as immunogens. The conversion of carbohydrate epitopes to peptide mimotopes is one means to overcome the T cell-independent nature of carbohydrate antigens because peptides have an absolute requirement for T cells. Although such conversion has great potential for the development of veterinarian and human vaccines, there are issues related to the use of peptide-based immunogens as functional surrogates. Some of these issues are fundamental, pertaining to how mimicry comes about at the molecular level, and some are application oriented, directed at elucidating important immunological mechanisms. In this article the potential and caveats of this technology regarding its application in vaccine discovery are analyzed.