Here we show that the low temperature phase of magnetite is associated with an effective, although fractional, ordering of the charge. Evidence and a quantitative evaluation of the atomic charges are achieved by using resonant x-ray diffraction (RXD) experiments whose results are further analyzed with the help of ab initio calculations of the scattering factors involved. By confirming the results obtained from x-ray crystallography we have shown that RXD is able to probe quantitatively the electronic structure in very complex oxides, whose importance covers a wide domain of applications.