Quercetin (Q) and rutin (R) are well known and most studied flavonoids due to their activities in reduction of inflammation, oxidative damage, platelet aggregation and inhibition of cancer proliferation. Despite their remarkable potentials they have limited oral bioavailability due to the low water solubility. Therefore in this study inclusion complexes of Q and R with hydroxypropyl-beta-cyclodextrin (HP-beta-CD) were formulated to improve the aqueous solubility, antiproliferative efficacy and also antioxidant activity of the flavonoids. According to the analyses results, aqueous solubilities of Q and R were increased up to ~630 fold and ~55 fold, respectively. ZP values were ranged between -21.7 +/- 0.3 mV and -6.1 +/- 0.8 mV showing the anionic structure of the complexes. 1HNMR analyses revealed the complex formation considering the shifts of the protons of the APIs as well as HP beta-CD. The in vitro release analyses revealed that the cumulative release of Q was decreased from 22.9 % to 18.1 and 15.2 for T9 and T 24 formulations respectively while the cumulative release of R increased from 26.8 % up to 64.5 % and 75.8 % with T14 and T24 formulations respectively. According MTT analyses results, Q showed higher antiproliferative effect in MDA-MB-231 and A549 cell lines compared to NIH-3T3 cell lines while R showed remarkable effect only on MDA-MB-231 cell lines at the end of 48 h of incubation period. A synergistic effect was observed in the formulation of combined flavonoid (Q/R) inclusion complexes and an antiproliferative effect was ordered as MDA-MB-231 > A549 > NIH-3T3. The selected complexes T9 (Q), T14 (R) and T24 (Q/R) have shown the highest antioxidant activity with 93.8 %, 65.3 % and 93.1 % respectively with DPPH analyses. In conclusion incoporation of Q, R and Q/R to HP-beta-CD based inclusion complexes have great potentials with enhanced in vitro dissolution characteristics and antiproliferative effects on different types of cancer cell lines for efficient treatment of severe disorders.