We prepared and characterized the inclusion complexes of daidzein with poly(amidoamine) (PAMAM) and poly(propylene imine) (PPI) dendrimers. Aqueous solubility of daidzein was significantly enhanced by both PAMAM and PPI (186- and 650-fold at 0.36 mM, respectively). Daidzein in G3 PAMAM solution is more stable than that in G4 PPI. NMR studies reveal the encapsulation of daidzein within the interior cavities of PPI through hydrophobic interactions. Daidzein exhibits a slower release behavior from PPI than that from PAMAM. PPI/daidzein complex is much more toxic than PAMAM/daidzein complex on several cell lines. PAMAM/daidzein complexes showed similar protective effect on oxidative stress-induced cytotoxicity as compared to free daidzein. These results suggest that the inclusion of daidzein with dendrimer can effectively improve the solubility, prolong the delivery, and maintain the anti-oxidant activity of daidzein. This research provides new insights into dendrimer-based drug delivery systems and will be helpful for the design of novel dendrimer/drug formulations.