High-energy ball milling of anatase (a) TiO 2 and 20mol% monoclinic (m) ZrO 2 mixture at different durations results in formation of nanocrystalline high-pressure srilankite (s) TiO 2 polymorph at initial stage of milling. Formation of another rutile (r) TiO 2 polymorph in nanocrystalline form is noticed in samples milled for longer duration in expense of s-TiO 2 phase. Nanocrystalline cubic (c) ZrO 2 is formed from m-ZrO 2 –a-TiO 2 solid solution. Microstructure of the unmilled and ball-milled samples has been characterized by Rietveld's method of structure refinement of X-ray powder diffraction data and by direct observations using FE-SEM and HR-TEM. Particle size, rms lattice strain, change in lattice parameters and phase content of individual phases have been estimated from Rietveld's analysis. A comparative study of microstructure revealed from direct observations corroborates the findings of X-ray diffraction study in all respects. At higher milling time, nanocrystalline particles are heavily agglomerated and it becomes difficult to estimate the microstructure from such samples. It has been pointed out that the X-ray diffraction is a better method for microstructure characterization of heavily deformed nanocrystalline multiphase materials.