The recombinant fusion proteins hybrid 1 [H1 (Ag85B-ESAT-6)] and hybrid 56 [H56 (Ag85B-ESAT-6-Rv2660c)] derived from Mycobacterium tuberculosis are promising antigens for subunit vaccines against tuberculosis. Both antigens are early batches of antigens to be enrolled in human clinical trials and it is therefore important to characterize their conformational stability in solution as well as upon interaction with adjuvants. In this study, the physical stability of the two antigens was characterized using a number of biophysical techniques. Dynamic light scattering and sodium dodecyl sulfate-polyacrylamide gel electrophoresis analyses demonstrated that both antigens exist as a distribution of multimeric states under nonstressed conditions. Their conformational stability was monitored as a function of pH and temperature and visualized in three-index empirical phase diagrams. Both antigens showed a gradual loss of secondary as well as tertiary structure as a function of temperature, with no cooperative transitions observed. Preformulation studies with the Th1-inducing cationic adjuvant CAF01 showed that the antigens were almost completely surface adsorbed. Upon adsorption, the liposome size increased; however, the physical stabilities of the bound and the unbound antigens were comparable. This study provides important information about the biophysical properties of H1 and H56 and highlights the analytical challenges of characterizing complex vaccine formulations.