We used several approaches to develop enhanced vaccines for chronic viral infections such as human immunodeficiency virus (HIV) and hepatitis C virus (HCV), I) Selected epitopes were used to avoid potentially harmful immune responses. 2) Linkage between helper and cytotoxic T‐lymphocyte (CTL) epitopes was found to be important, 3) We developed an “epitope enhancement” approach modifying the sequences of epitopes to make more potent vaccines, including examples for HIV and HCV epitopes presented by murine class II and human class I major histocompatibility complex (MHC) molecules, 4) CTL avidity was found to be important for clearing viral infections in vivo, and the mechanism was examined. High‐avidity CTLs, however, were found to undergo apoptosis when confronted with high‐density antigen, through a mechanism involving tumor necrosis factor (TNF), TNF‐RII, and a permissive state induced through the T‐cell receptor. 5) We employed cytokines in the adjuvant to steer immune responses toward desired phenotypes, and showed synergy between cytokines, 6) Intrarectal immunization with pep‐tide vaccine induced mucosal and systemic CTL, Local mucosal CTL were found to be critical for resistance to mucosal viral transmission and this resistance was enhanced with mucosally delivered interleukin‐12, 7) We used an asymmetry in induction of mucosal and systemic immune responses to circumvent pre‐existing vaccinia immunity for use of recombinant vaccinia vaccines.