Sodium dodecyl sulfate polyacrylamide electrophoresis (SDS-PAGE) is the most widely used method to carry out analytical separations of small poly-peptides and proteins. Despite its recognized importance, our understanding of the transport of surfactant denatured proteins during electrophoresis is based greatly on assumptions of protein conformation inside the gel and on macroscopic measurements of their mobility. We have recently designed and built a new cell that allows us to perform small angle neutron scattering (SANS) measurements during the process of electrophoresis. Contrast-variation SANS is used to provide, for the first time, a structural picture of the conformation of protein-surfactant complexes during this separation process. Our recent SANS observations are discussed and related to transport models (Ogston model and reptation model) that have been proposed to occur during SDS-PAGE.