The absolute configuration of secondary hydroxy functions of seven natural occurring polyyne derivatives has been elucidated by the application of Mosher method of diastereomeric methoxy-2-trifluoromethyl-phenylacetyl (MTPA) ester formation. High-performance liquid chromatography with diode array detection (HPLC-DAD) of the reaction mixture using a water/acetonitrile gradient allowed monitoring the reaction progress. Coupling of high-performance liquid chromatography to solid-phase extraction combined with nuclear magnetic resonance (HPLC-SPE-NMR) was utilized to generate highly reproducible (1)H and (19)F NMR data needed as input for the absolute configuration determination based on the analysis of relative shift differences. Chromatographic peaks of reaction substrates and reaction products bearing less 10mug analyte were trapped on SPE cartridges with the aid of water as makeup solvent. Deuterated chloroform was used to elute and transfer the peak content from the SPE to the 60mul flow cell of a 500MHz NMR spectrometer. For each analyte (1)H NMR spectra were obtained within 15min. Additionally (19)F NMR spectra were recorded for selected analytes in the same timeframe. Based on the obtained NMR data, the absolute configuration of all polyynes under investigation was successfully designated.