The generation of modified lantibiotics in whole cells has proved to be of value for the investigation of the specificity of the lantibiotic-processing enzymes and their tolerance to mutations in the primary sequence of lantibiotics. The development of methods to produce new lantibiotic variants has also enabled the investigation of the structure-activity relationships of these compounds and hence an evaluation of this hitherto underexploited class of natural products as a source of potential therapeutic drug candidates. We report the methods and strategies that have been used to engineer new lantibiotic variants and practical methods to analyze libraries of new compounds with a view toward optimizing drug properties.