The hepatitis C virus (HCV) envelope glycoprotein E1 has been widely employed as a potential vaccine antigen in clinical research. A truncated form (amino acids 192-326) of the E1 protein (E1y) was expressed in the yeast Hansenula polymorpha and purified from the cell lysate. E1y forms protein particles in the absence of detergent and remains monomeric when detergent concentration is high. In this work, a variety of spectroscopic and hydrodynamic techniques including circular dichroism, intrinsic and ANS fluorescence as well as static and dynamic light scattering are employed to evaluate E1y structural stability. The effect of two dissociative detergents, Empigen BB and Zwittergent 3-12 on E1y stability, is investigated and the results are summarized using the empirical phase diagram (EPD)-based approach. The EPDs reveal that when temperature is increased, E1y particles are more thermally stable than monomers at both pH 5 and 7. A more detailed biophysical characterization of the E1y particles is also performed including pH and temperature as variables. The EPD indicates that E1y particles are most stable at pH 7 and 8 under the given experimental conditions. The results from this study provide detailed information that will help guide the future development of E1-based HCV vaccines.