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We present the new promising nanostructure- sandwich-like mesoporous silica nanoflakes synthesized on graphene oxide sheets core. In the first step biocompatibility of the nanoflakes with PEG and without functionalization in human fibroblast, melanoma and breast cancer cells was assessed. In order to define the cellular uptake in vitro and biodistribution in vivo the nanostructures were labelled with fluorescent dye. In the next step, the silica nanostructures were filled by the anticancer drug- methotrexate (MTX) and cytotoxicity of the complex in reference to MTX was evaluated. The WST-1 assay shows mild, but concentration dependent, cytotoxicity of the nanoflakes, most significant for the non-functionalized structures. PEG-modified silica nanoflakes didn't produce a disruption of cell membranes and lactate dehydrogenase (LDH) release. Cell imaging revealed efficient internalization of the silica nanoflakes in cells. Ex vivo organ imaging showed high accumulation of the nanostructures in lungs, bladder and gall bladder, whereas confocal imaging revealed wide nanoflake distribution in all tested tissues, especially at 1 h and 4 h post intravenous injection. Cytotoxicity of the nanoflake-MTX complex in reference to MTX showed similar cytotoxic potential against cancer cells. These findings may provide useful information for designing drug delivery systems, which may improve anticancer efficacy and decrease side effects.