On the basis of the exclusive existence of homochirality in biomolecules and the well-known phenomenon of chiral recognition, it is obvious that chirality is a crucial factor in biological events. We report here that supramolecular assemblies of peptide amphiphiles interact with lipid bilayer membranes in a stereospecific manner. When negatively charged chiral phospholipid bilayer vesicles were subjected to the assemblies, we found that peptide amphiphiles with l-amino acids show stronger affinity for the liposomes compared to the ones with d-amino acids. To examine their biological functions, we tested the cytotoxicity of nanofibers against mammalian primary cells using human bone marrow mesenchymal stem cells and murine astroglial cells. We demonstrated that cell viability increased when d-amino acids were incorporated in the structure of peptide amphiphiles, which is consistent with our finding of their weaker interactions with lipid bilayer membranes.