Daidzein (DAZ), a dominant isoflavone in various natural products such as soybeans, has been gaining attention due to the beneficial health effects (e.g., protection against cancer and diabetes) of its metabolites. Our major hypothesis was that dietary exposure to the soy phytoestrogen DAZ could modulate the immune responses toward a protective effect and lead to improved metabolic functions (such as glucose metabolism). In this study, we applied complementary mouse models, the hybrid B6C3F1 and inbred type 1 diabetes prone non-obese diabetic (NOD) mice, to investigate if DAZ exposure modulated the immune responses. The animals were orally administered DAZ at various physiological doses (2-20 mg/kg body weight) during adulthood. DAZ significantly altered the relative organ weights in female B6C3F1 mice and decreased the B cell population (represented by CD3-IgM+), while the T cell populations (represented by CD3+IgM-, CD4+CD8- and CD4-CD8+) were increased. In addition, DAZ dosing produced a decrease in the percentage of late apoptotic thymocytes. However, the activities cytotoxic T cells and natural killer cells were not altered in the B6C3F1 mice. In NOD mice, the blood glucose level and glucose tolerance were not affected by DAZ exposure, but DAZ modulated the antibody production, as shown by increased levels of IgG2b in NOD females and IgG1 in NOD males. Further, DAZ increased CD8+CD25+ splenocytes in NOD females. Taken together, DAZ induced an immunomodulatory effect in both NOD and B6C3F1 mouse strains; however, minimal effects on glucose homeostasis were observed.