Our objective in this work was to identify the structural basis for the molecular recognition of peptides by peptide transporters. Various assays for dipeptide transport by the dipeptide and tripeptide permeases of Escherichia coli were performed, together with measurements of thermodynamic parameters of substrate binding to the dipeptide binding protein using isothermal titration calorimetry. Computer-based conformational analysis of the test dipeptides was performed to define the repertoire of conformers that each dipeptide adopts in solution. Strict correlations were identified between the complement of particular conformers adopted by a peptide and its bioactivity as a substrate for each transporter. Details of the structural and electronic parameters that define the molecular recognition templates (MRTs) of the dipeptide substrates of these transporters are presented; similar MRTs are likely to apply with dipeptidases. These MRTs provide the essential information for the rational design of peptide-based drugs tailored for exploitation of peptide transporters in microorganisms and man.