The large number of potential applications of ionic liquids (ILs) requires an understanding of their environmental impacts including their adverse effects on microorganisms living in soil and water. The molecular mechanism of toxic activities of these liquids is yet to be understood in detail. Any foreign molecules, interacting with an organism, have to encounter first the cellular membrane, which is predominantly composed of the lipid bilayer. In this work, multilamellar vesicles (MLV) of phospholipids have been used to shed light on the effect of an IL on the structure of a cellular membrane. The MLVs formed by the zwitterionic lipid, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) are found to shrink as a consequence of interaction with an imidazolium-based IL, 1-decyl-3-methylimidazolium tetrafluoroborate ([DMIM] [BF 4 ]). The absorbed ILs significantly modify the surface charge of the MLVs. While these observations indicate a strong membrane-IL interaction, synchrotron-based small angle X-ray diffraction (SAXD) measurements provide a structural description of the interaction. SAXD and Fourier transform infrared spectroscopy studies clearly reveal a disordering effect of the IL on the conformational organization of the lipid chains. The presence of the negatively charged lipid 1,2-dipalmitoyl-sn-glycero-3-phospho-l-serine sodium salt (DPPS) in MLVs plays an important role in disordering the chains in the membrane and inter-bilayer interactions. © 2018, European Biophysical Societies' Association.