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The detailed understanding of the crystal structure and microstructure of nanomaterials is useful to predict the properties of nanomaterials. SnO2 nanocrystals of different shapes like particles, spheres, rods and pyramids are chemically synthesized. Here, we report the crystal structure and microstructure of SnO2 nanocrystals of different morphologies using X-ray diffraction and high-resolution transmission electron microscopy (HRTEM). It is interesting to note that the tetragonal phase is found in particle, sphere and rod shaped SnO2 nanocrystals and pyramid shaped nanocrystals are composed of two types of orthorhombic phases. The Rietveld method has been used for refining simultaneously the atomic structure and microstructure of different SnO2 nanocrystals, and the growth mechanisms in different shapes are found to be different due to different preferential growth. Structural defects such as oxygen vacancies, deformation of unit cell and more importantly texturing effects are associated with change in bond length, bond angle and crystallite morphology. Size and lattice strain of different kinds of SnO2 nanocrystals are also studied in detail by using the Rietveld method of analysis and transmission electron microscopy (TEM). [ABSTRACT FROM AUTHOR]