The substrates of the peptide transporters PEPT1 and PEPT2 range from di- and tripeptides to peptidomimetic drugs. Due to their localization, PEPT1 and PEPT2 can be utilized for the oral or pulmonary administration of drugs. Therefore, the knowledge of the structural requirements that are essential for the recognition by the H+/peptide symporters is of pharmaceutical interest for a targeted drug design. Since the 3D-structures of PEPT1 and PEPT2 are unknown, three dimensional quantitative structure-activity relationship analyses (3D-QSAR) of PEPT1- and PEPT2-ligands have been carried out to derive the recognition elements of β-lactam antibiotics that are required for the binding to PEPT1 and PEPT2. Besides a number of β-lactam antibiotics the data sets contained also structurally related di-and tripeptides. In the first part of the work the binding affinities of PEPT1 and PEPT2 ligands, in particular those of tripeptides, were measured at cell lines expressing PEPT1 and PEPT2, respectively. Subsequently, robust and statistically significant CoMSIA models (Comparative Molecular Similarity Indices Analysis) have been generated for ligands of PEPT1 and PEPT2. These models can be used to explain different binding affinities of the ligands and to predict the Ki-values of new substrates of PEPT1 and PEPT2. The comparison of the molecular fields of the CoMSIA-models allows the explanation of differences in the substrate binding between PEPT1 and PEPT2. The interpretation of the CoMSIA models led to a novel ligand of PEPT1 and PEPT2. 2-aminothiazole-4-acetic acid (ATAA) binds with low affinity to PEPT1 and PEPT2. Derivatives of ATAA showed different binding affinities to the peptide transporters which suggested further differences in substrate binding by PEPT1 and PEPT2. These results are of importance for the utilization of the H+/peptide symporters as a drug delivery system.