The presence of high-avidity CTLs in the right compartment can greatly affect clearance of a virus infection (for example, AIDS viral infection of and dissemination from mucosa). Comparing mucosal vs systemic immunization, we observed a novel compartmentalization of CTL avidity and proportion of functionally active Ag-specific CD8+ T cells to tissues proximal to sites of immunization. Whereas both sc and intrarectal routes of immunization induced tetramer+ cells in the spleen and gut, the mucosal vaccine induced a higher percentage of functioning IFN-γ+ Ag-specific CD8+ T cells in the gut mucosa in mice. Translating to the CD8+ CTL avidity distribution in rhesus macaques, intrarectal vaccination induced more high-avidity mucosal CTL than sc vaccination and protection of mucosal CD4+ T cells from AIDS viral depletion, whereas systemic immunization induced higher avidity IFN-γ-secreting cells in the draining lymph nodes but no protection of mucosal CD4+ T cells, after mucosal challenge with pathogenic simian/human immunodeficiency virus. Mucosal CD4+ T cell loss is an early critical step in AIDS pathogenesis. The preservation of CD4+ T cells in colonic lamina propria and the reduction of virus in the intestine correlated better with high-avidity mucosal CTL induced by the mucosal AIDS vaccine. This preferential localization of high-avidity CTL may explain previous differences in vaccination results and may guide future vaccination strategy.