Biological membrane structure is inherently complex, and understanding the structure of peptide chains inserted in membranes is vitally important for the development of effective diagnosis and treatments of diseases. Surface Enhanced Raman Spectroscopy (SERS) was used as a tool for studying lipid membrane structure in a natural fluid, room temperature environment. Gold nanostructures focus light to a molecular length scale at their surface, creating the possibility to visualize molecular structure. Optical excitation of gold nanoparticles at their size and shape-dependent plasmon resonant frequency induces strong oscillations of the nanoparticle’s free electron gas, leading to SERS – an enhancement of Raman scattering signals in a distance dependent manner at the molecular scale. This project utilizes gold nanorods, tuned to an excitation laser wavelength of 785 nm, as a substrate for lipid membranes so that their structure can be analyzed by SERS. The surfactant cetyltrimethylammonium bromide (CTAB) that stabilizes nanorods was exchanged with the biologically relevant lipid dioleoylphosphatidylcholine (DOPC), and the insertion of the peptide residue tryptophan into the lipid membrane was observed using SERS for confirmation. Full characterization of the lipid membranes was carried out, demonstrating a well ordered, gold supported bilayer. SERS spectra also contain information on molecular position and orientation relative to the surface, but are difficult to interpret quantitatively. An analysis method that combines SERS and unenhanced Raman spectra with theoretical calculations of the optical field and molecular polarizability is introduced. Together these reveal the molecular orientation and position of surfactant layers on gold nanorods and of tryptophan in phospholipid bilayers. This method offers a new approach to analyzing lipid membrane molecular structure under ambient conditions, with microscopic quantities, and without molecular labels.