Molecular recognition is one of the most important phenomena in Chemistry and Biology. Here we present a new way of enantiomeric molecular recognition using intrinsically chiral semiconductor nanocrystals as assays. Real-time confocal microscopy studies supported by circular dichroism spectroscopy data and theoretical modelling indicate an ability of left-handed molecules of cysteine and, to a smaller extent, histidine and arginine to discriminate between surfaces of left- and right-handed nanocrystals.