As an initial step in the development of a second-generation smallpox vaccine derived from the Lister strain, to be prepared for a variola virus threat, diversity of the traditional vaccine was examined by characterizing a series of ten viral clones. In vitro and in vivo phenotypic studies showed that the biological behavior of the clones diverged from each other and in most cases diverged from the vaccinia virus (VACV) Lister parental population. Taken together, these results demonstrate the heterogeneity of the viral population within the smallpox vaccine and highlight the difficulty in choosing one clone which would meet the current requirements for a safe and effective vaccine candidate.