The study of individuals who are able to achieve durable control over human immunodeficiency virus (HIV) replication in the absence of antiretroviral therapy has become increasingly important in light of recent vaccine trials which have failed to induce protective immunity. Understanding the correlates of protection in these HIV “controllers” would aid in both the rational design of potential vaccine candidates and the testing of their efficacy. Cell-mediated immune responses, in particular HIV-specific CD8+ T-cell responses, have been shown to be critical in decreasing the initial viremia after acute infection and determining the chronic infection set point (32, 33, 43). These responses have proven to be “too little and too late” to prevent the establishment of chronic infection; however, studies of HIV-specific CD8+ T-cell responses in controllers suggest that strong, polyfunctional responses may be important in long-term virologic control (1, 6, 11, 15, 16, 44). In addition, the association of controller status with class I HLA alleles, predominantly HLA-B27 and HLA-B57, has been well documented in multiple cohorts (2, 9, 13, 39). The maintenance of robust HIV-specific CD4+ T-cell responses may also favor long-term control of HIV replication in untreated persons. One of the primary roles of CD4+ T cells is to provide “help” to CD8+ T cells. Many studies have shown that proper functioning of CD4+ T cells is necessary for high-quality antigen-specific CD8+ T-cell responses (3, 28, 29, 38, 58). HIV-specific CD4+ T cells in the peripheral blood of long-term nonprogressors (LTNP) have been shown to be polyfunctional, producing both gamma interferon (IFN-γ) and interleukin-2 (IL-2), whereas those from progressors tend to be monofunctional, secreting only IFN-γ (7, 14, 21, 22, 44). Additionally, the ability of CD4+ T cells to proliferate appears to be preserved in controllers (46, 56). The maturation status of CD4+ T cells that function in the context of HIV infection may also be important, as individuals who are able to preserve central memory T cells and sustain an activated effector memory CD4+ T-cell population are better able to suppress viral replication (45). Much less is known about the association of class II HLA alleles and controller status; however, a few studies have cited a relationship between HLA-DRB1*13 and/or HLA-DQB1*06 and HIV control (10, 31, 36, 55). Previously, we have shown that CD8+ T cells from the rectal mucosa of controllers with protective class I alleles (HLA-B13, -B27, -B57, -B58, and -B81) are highly polyfunctional compared to CD8+ T cells from either controllers or noncontrollers (NC) lacking these alleles (16). Additionally, we found that mucosal CD8+ T-cell responses from individuals who had protective class I alleles in combination with the class II alleles HLA-DRB1*13 and/or HLA-DQB1*06 were of greater magnitude than mucosal CD8+ T-cell responses from those who had protective class I alleles alone (16). Therefore, we wanted to specifically examine HIV-specific mucosal CD4+ T-cell responses among controllers with and without these potentially protective class II HLA alleles. Our hypothesis was that controllers, particularly those who possessed HLA-DRB1*13 and/or HLA-DQB1*06, would have more robust and polyfunctional HIV-specific CD4+ T-cell responses than noncontrollers or subjects on highly active antiretroviral therapy (HAART) and that these responses would correlate with strong CD8+ T-cell responses in the same individuals. We found that, indeed, controllers generally had stronger HIV-specific CD4+ T-cell responses than other groups in rectal mucosa and that, among controllers, those with the haplotype HLA-DRB1*13/HLA-DQB1*06 had particularly high percentages of polyfunctional HIV-specific CD4+ T cells in rectal mucosa. Furthermore, the proportion of polyfunctional mucosal CD4+ T cells directly correlated with the total magnitude of the mucosal CD8+ T-cell response. These data collectively suggest that the preservation or expansion of both HIV-specific CD4+ and CD8+ T cells may be an important mechanism whereby certain controllers maintain durable control of HIV replication.