The heterogeneous structure of synaptic vesicles isolated from rat brain is investigated considering solution small-angle x-ray scattering data in combination with data obtained by cryogenic electron microscopy, dynamic light scattering and biochemical analysis. Overall low resolution structural models of the entire functional synaptic vesicle are proposed, elucidating details on the density profi le of the membrane, including contributions from the lipids and the proteins, as well as addressing the average conformation and overall lateral organization of proteins in micro-domains on the average synaptic vesicle under quasi-physiological conditions. Entropic contributions to free energy due to possible protein cluster formation and disintegration on the synaptic vesicle are investigated. Further, cell free fusion systems are characterized employing dynamic light scattering and applicability of small-angle x-ray scattering is considered for investigating membrane fusion processes.