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The three-dimensional structure of oleic acid-capped CdSe and thiol-capped CdTe nanocrystals used as quantum dots has been determined by total synchrotron radiation x-ray diffraction and atomic pair distribution function analysis. Both CdSe and CdTe are found to exhibit the zinc-blende-type atomic ordering. It is only slightly distorted in CdSe implying the presence of nanosize domains and very heavily distorted in CdTe due to the presence of distinct core-shell regions. The results well demonstrate the great potential of the experimental approach and thus encourage its wider application in quantum dot research.