During the use of chiral 2-oxo-1,3,2-dioxaphosphorinanes as derivatizing reagents in the enantiomeric excess determination of amines, alcohols, and unprotected amino acids, minor traces of side reaction products were observed by 1H and 31P NMR spectroscopy. Analysis of the reaction mixture showed that the side products are in fact diphosphates and several intermediates leading to their formation. From an analytical, mechanistic, and stereochemical point of view, the study of unexpected new reaction intermediates leading to diphosphates is of particular interest. Due to the easy structural modification of the starting materials in both enantiomerically pure and racemic forms as well as easy access to oxygen-labeled materials for complete structural elucidation of both intermediates and diphosphates, we accomplished a complete structural analysis. Also a mechanistic proposal for their formation proved possible using 1D and 2D 1H and 31P NMR techniques as well as the X-ray data of both starting material and two of the products.