Mesoporous silica material type SBA-15 was modified with different amounts of Zn (2 and 4 wt. %) by incipient wetness impregnation method in ethanol. The parent, Zn-modified and quercetin loaded samples, were characterized by XRD, N2 physisorption, TEM, thermal gravimetric analysis, UV-Vis and FT-IR spectroscopies and in vitro release of quercetin at pH 5.5 which is typical of dermal formulations. By this loading method anhydrous quercetin was formed on the silica carrier. It was found that the different hydrate forms of quercetin (dihydrate, monohydrate, anhydrite) significantly influence the physico-chemical properties of the delivery system. It was found that hydrate forms of quercetin can be differentiated by XRD and by FT-IR spectroscopic methods. Thus, by evaluating the interaction of the drug with the silica carrier the changes due to its hydration state always have to be taken into account. Formation of Zn-quercetin complex was evidenced on zinc modified SBA-15 silica by FT-IR spectroscopy. High quercetin loading capacity (over 40 wt. %) could be achieved on the parent and Zn-containing SBA-15 samples. The in-vitro release process at pH=5.5 showed slower quercetin release from Zn-modified SBA-15 samples compared to the parent one.Additionally, the comparative cytotoxic experiments evidenced that quercetin encapsulated in Zn-modified silica carriers has superior antineoplastic potential against HUT-29 cells compared to free drug. Zn-modified SBA-15 silica particles could be promising carriers for dermal delivery of quercetin.