The microstructure and thermal stability of plastically deformed Al-5.9Mg-0.3Sc-0.18Zr alloy have been investigated. Severe plastic deformation has been performed by high-pressure torsion (HPT) straining at room temperature. The microstructure as a function of the number of rotations is studied by X-ray diffraction peak profile analysis. It is concluded that the HPT technique results in a nanostructure with about 40 nm crystallite size. The crystallite size first decreases with the number of rotations, however, after five turns it reaches saturation. The dislocation density increases with turns and the character of the dislocations becomes more edge type. The thermal stability of the nanostructure is studied by differential scanning calorimetry. The stored energy increases with the number of rotations and the maximum of the exothermal peak was shifted to higher temperatures. Increasing the temperature of the heat treatment, the dislocation density decreases faster than the increase of the mean crystallite size.