The potential biomedical applications of ionic liquids (ILs) need an understanding of the effects of the molecules in living organisms. Researchers are still exploring the molecular level description of this interaction. Any foreign molecule affecting a living organism has to interact first with the outer layer of a cell, which is mainly composed of a phospholipid bilayer. Here, to understand the membrane-IL interaction, a zwitterionic lipid has been chosen to prepare multilamellar vesicles (MLVs) which are the model cellular membranes. Small angle x-ray diffraction study has revealed the change in inter-bilayer spacing in the presence of imidazolium based ILs in the ripple phase of the bilayer. The investigation was extended further to understand the role of a negatively charged lipid in the MLVs. This study indicates that the cations of an IL screen electrostatic repulsion between the negatively charged lipids and induce the formation of a vesicle. © 2020 American Institute of Physics Inc.. All rights reserved.