Quercetin (Q) and rutin (R) are plant-originated polyphenolic flavonoids with considerably strong antioxidant and anticancer activity. Despite their potentials, low water solubility, stability problems and oral bioavailability limit their therapeutic use. The specific purpose of our study was to formulate inclusion complexes of Q and R with β-cyclodextrin (β-CD) to improve the solubility and also antioxidant activity of the flavonoids. Therefore 12 different complexes were prepared by both evaporation and lyophilization methods with 1:1 molar ratio in ethanol:water (1:1, v/v) solvent system. The characteristics of the complexes were also evaluated by yield%, zeta potential (ZP), entrapment efficiency (EE), 1H NMR, XRD, FT-IR, DSC analyses. In vitro dissolution studies were performed in comparison with pure substances. Antioxidant activity studies were carried out with DPPH tests. Cytotoxic evaluations of complexes were conducted with MTT tests on NIH 3T3, MDA-MB-231 and A549 cell lines. 1H- NMR analyses revealed the complex formation considering the shifts of the protons of the APIs as well as β-CD. ZP values were ranged between -21.20±0.56 mV and -7.10±0.62 mV. The aqueous solubility of Q and R were increased ∼29 fold and ∼35 fold, respectively. According to the MTT analyses results it has been shown that the flavonoids loaded complexes were particularly effective in MDA-MB-231 cells and 50% cell inhibition was observed even at 5 µM. The results of the analyses have demonstrated that the formation of inclusion complexes resulted in enhanced water solubility and cytotoxicity which will enhance their potential use in pharmaceutical applications.