Gp90 and gp45 synthetic peptides, which mimic conserved sequences of native viral proteins, are recognized by antibodies to equine infectious anemia virus (EIAV) in asymptomatic carrier horses and generate humoral and cellular responses in immunized mice. Cytokine mRNA levels were evaluated in equine peripheral blood mononuclear cells (PBMCs) after in vitro stimulation with gp90 and gp45 with the aim of determining the cytokine profile associated with the proliferative response. Stimulation index (SI) values indicate that 100 and 60% of EIAV-infected horses recognized gp90 and gp45, respectively. A strong positive correlation was found between IL-12p40 and SI, IFN-gamma and SI, and IL-12p40 and IFN-gamma (p < 0.001). These results suggest the presence of specific memory cells that would contribute to maintain reinfection resistance and that conserved viral regions represented by gp90 and gp45 synthetic peptides may be good candidates for inclusion in vaccine strategies against EIAV.