Because of their amphiphilic nature, lipids tend to self-assemble into membranes and other topologically complex structures that can serve a number of functions in both natural and synthetic environments. The structure of lipid assemblies often varies on length scales of 2-100 nm, and morphological studies of such structures often require electron-optical methods. Image contrast in an electron microscope is usually generated by large defocus for unstained samples or by positive/negative staining methodologies. We currently are developing alternate approaches to generate image contrast based on spatially resolved Electron Energy Loss Spectroscopy (EELS) [1]. This has allowed us to distinguish between different lipid species as well as between lipids and protein. Low-loss spectra taken from cholesterol, ceramide and protein (BSA) show that these materials have characteristic spectroscopic fingerprints due to both π and σ valence-electron excitations that are sufficiently different to distinguish between them.