The effect of mechanical alloying on the microstructure of atomized 6061 aluminium alloy powder and 6061 powder with a zirconium addition was studied in the work. The atomized 6061 aluminium alloy powder and 6061 powder with addition of 2 wt.% Zr were milled in a planetary ball mill and investigated using X-ray diffraction measurements, conventional and high-resolution electron microscopy (TEM/HRTEM) and high-angle annular dark field scanning transmission electron microscopy combined with energy dispersive X-ray microanalysis. An increase of stresses was observed in milled powders after the refinement of crystallites beyond 100 nm. In the powder with zirconium addition, some part of the Zr atoms diffused in aluminium forming a solid solution containing up to 0.5 wt.% Zr. The remaining was found to form Zr-rich particles containing up to 88 wt.% Zr and were identified as face centred cubic (fcc) phase with lattice constant a= 0.48 nm. That fcc phase partially transformed into the L1(2) ordered phase. Eighty-hour milling brought an increase of microhardness (measured with Vickers method) from about 50 HV (168 MPa) for the initial 6061 powder to about 170 HV (552 MPa). The addition of zirconium had no influence on the microhardness.