It is observed in this study that the chirality of cysteine stabilizers has a distinct effect on both the growth kinetics and the optical properties of CdTe nanocrystals synthesized in aqueous solution. The effect was studied by circular dichroism spectroscopy, temporal UV-vis spectroscopy, photoluminescence spectroscopy, and several other microscopy and spectroscopic techniques including atomic modeling. Detailed analysis of the entirety of experimental and theoretical data led to the hypothesis that the atomic origin of chiral sites in nanocrystals is topologically similar to that in organic compounds. Since atoms in CdTe nanocrystals are arranged as tetrahedrons, chirality can occur when all four atomic positions have chemical differences. This can happen in apexes of nanocrystals, which are the most susceptible to chemical modification and substitution. Quantum mechanical calculations reveal that the thermodynamically preferred configuration of CdTe nanocrystals is S type when the stabilizer is D-cysteine and R type when L-cysteine is used as a stabilizer, which correlates well with the experimental kinetics of particle growth. These findings help clarify the nature of chirality in inorganic nanomaterials, the methods of selective production of optical isomers of nanocrystals, the influence of chiral biomolecules on the nanoscale crystallization, and practical perspectives of chiral nanomaterials for optics and medicine.