Using 31P NMR spectroscopy as a tool, we investigated the condensation of H-phosphonoselenoate monoesters with a hydroxy component in the presence of various coupling agents. On this basis, synthetic protocols that eliminate or significantly suppress side reactions which might occur during the condensation in synthesis of H-phosphonoselenoate derivatives, have been developed. Absolute configuration of the produced dinucleoside H-phosphonoselenoates has been determined by stereochemical correlation analysis.