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Graphite oxide (GO) – a layered material formed by oxidized graphene planes – is applied widely as a precursor for preparation of various graphene based materials. Of particular interest are graphene oxide membranes which were found to possess unique selective permeability for liquids and hydrated ions, so they can be considered as perspective materials for water desalination and water treatment. In spite of high practical prospects, the physical foundations of amazing properties of GO-based materials have not yet been established. For this reason, the manufacture of materials with desired properties is made mainly by trial and error. The study of the molecular structure of swelled graphite oxide and graphene oxide membranes was hindered for a long time by lack of suitable experimental methods. In the report it will be shown that the nitroxide spin probe technique can be the useful instrument for detail investigation of GO-based systems and for estimation of relationship between molecular organization and macroscopic properties of GO materials. To date, this experimental method allowed us to find out a phase state of some liquids in the inter-plane space of graphite oxide, to clarify the mechanism of phase transformation like incongruent melting in the systems “GO powder – polar liquid”, to determine quantitatively the orientational ordering of GO membranes, and to measure pH value of water in between the oxidized graphene planes. The prospects of application of novel nitroxide radicals containing aromatic moieties for study of inner structure of GO membranes, as well as possibility of using of supercritical carbon dioxide for inserting of nitroxide radials into the membranes will be discussed.