Crystallographic analyses of DNA glycosylases bound to their cognate DNA substrates provide a rational basis for exploring the biochemical functions and substrate specificity of these proteins. Endo III and Ogg1 are members of the Endo III superfamily while Endo VIII and Fpg have the same novel fold. Ogg1 and Fpg share common structural motifs with Endo III and Endo VIII, respectively. By comparing the three dimensional structure of Fpg with Ogg1 and that of Endo III with Endo VIII—each complexed to its respective DNA substrate—we explore a central question in structural genomics, namely, how proteins with different tertiary structures perform identical biological functions. For DNA glycosylases, these include (a) binding to DNA and scanning the major groove for damage, ultimately forming a specific complex at the lesion site, (b) flipping the target base out of the DNA helix into a complementary pocket near the active site, and (c) nucleophilic attack at C1' accompanied by protonation of the heterocyclic ring to displace the damaged base.