The objective of this study is to understand the spatial organization of the tetrameric form of apolipoprotein E3 (apoE3), the major cholesterol transport protein in the plasma. We developed a fluorescence spectroscopic approach employing pyrene, a spatially sensitive probe that displays an excimer emission peak when it is proximal to another pyrene. It involved site-specific fluorescence labeling at pairs of cysteine residues introduced at defined distances on helix 2 of apoE3. The extent of emission peak intensity appears to depend on distance between pyrene moieties and the flexibility of the probes. Applying this approach to study the structural organization of the native tetrameric protein, we found that self-association via the C-terminal end juxtaposes the loop segment linking two domains of neighboring apoE3 molecules. Our study offers new insights into the conformation of apoE and presents the possibility of employing pyrene as a powerful fluorescent tool to study protein spatial organization.