Magnetite nanoparticles (Fe3O4) represent the most promising materials in medical applications. To favor high-drug or enzyme loading on the nanoparticles, they are incorporated into mesoporous materials to form a hybrid support with the consequent reduction of magnetization saturation. The direct synthesis of mesoporous structures appears to be of interest. To this end, magnetite nanoparticles have been synthesized using a one pot co-precipitation reaction at room temperature in the presence of different bases, such as NaOH, KOH or (C2H5)4NOH. Magnetite shows characteristics of superparamagnetism at room temperature and a saturation magnetization (Ms) value depending on both the crystal size and the degree of agglomeration of individual nanoparticles. Such agglomeration appears to be responsible for the formation of mesoporous structures, which are affected by the pH, the nature of alkali, the slow or fast addition of alkaline solution and the drying modality of synthesized powders.