The recognition and removal of damaged bases in the genome is the province of a highly specialized assemblage of enzymes known as DNA glycosylases. In recent years, structural and mechanistic studies have rapidly moved forward such that in some cases, the high-resolution structures of all stable complexes along the reaction pathway are available. In parallel, advances in isotopic labeling of DNA have allowed the determination of a transition state structure of a DNA repair glycosylase using kinetic isotope effect methods. The use of stable substrate analogs and fluorescent probes have provided methods for real time measurement of the critical step of damaged base flipping. Taken together, these synergistic structural and chemical approaches have elevated our understanding of DNA repair enzymology to the level previously attained in only a select few enzymatic systems. This review summarizes recent studies of the paradigm enzyme, uracil DNA glycosylase, and discusses future areas for investigation in this field.