Immunostimulatory molecules such as monophosphoryl lipid A (MPL), a Toll-like receptor 4 (TLR4) agonist, can be formulated to enhance vaccine adjuvant effects and to promote a Th1-type immune response. This study compares the in vitro and in vivo potency of aqueous and emulsion formulations containing a synthetic MPL analogue. In addition, formulation structure and association of the synthetic TLR-4 agonist and antigen with the formulation are characterized using dynamic light scattering, zeta potential measurement, HPLC, and SDS-PAGE. The biological and biophysical effects of formulating the agonist with different oil and surfactant components from animal, plant, and synthetic sources are examined. These findings have important implications for the formulation of TLR4 agonists as well as the influence of formulation component substitution on adjuvant activity. The results indicate that (1) the agonist is associated with the oil droplets in emulsion formulations, (2) the emulsion formulations containing synthetic TLR4 agonist induce higher IgG2a/IgG1 antibody ratios than aqueous formulations or an emulsion formulation without the agonist, and (3) appropriate plant-derived components can be substituted for animal-derived components in oil-in-water emulsions without loss of biological activity.