On the day of challenge, the frequency of circulating CD4+ T regulatory cells was significantly lower in the immunized monkeys than in normal controls. However, after challenge (PC), these cells expanded more rapidly and strongly in lymph nodes (LN) of the immunized macaques compared to the control macaques. In addition, at 3 days PC, the frequency of vaginal mucosal CD4+FoxP3+ cells increased in the immunized macaques (p < 0.05). In contrast, the frequencies of CD8+FoxP3+ T cells in tissues of immunized macaques did not increase PC, as they did in control monkeys. Differences in expression of pro-inflammatory and regulatory genes were detected in the immunized macaques compared to gene expression in normal, uninfected macaques at the time of challenge. IL-8, IL-17, CCL3 and TNF mRNA levels were significantly decreased in LNs and/or vagina of immunized macaques. IL-17 mRNA was up-regulated at the site of challenge on day 7 PC while in SHIV-immunized macaques it was down-regulated (p = 0.017). Finally, IL-6 increased over-time in tissues of the control, but not the immunized macaques PC.