High-performance liquid chromatography/atmospheric pressure chemical ionization mass spectrometry (HPLC/APCI-MS) is a very promising approach to structural investigations of positional isomers and stereoisomers. This method was applied successfully to stereoisomeric norditerpenoid alkaloids differing in configuration at C-6. APCI-MS allowed the easy and precise control of energy deposition by varying the drift voltage. Comparison of the breakdown curves, observed by changing the potential difference between the first electrode and the second electrode of the APCI ion source, revealed the stereochemical dependence of different fragmentations. Comparison of the APCI spectra showed that the abundance of fragment ions was significantly higher for C-6 beta alkaloid than for C-6 alpha alkaloid. The axial positions of the corresponding substituents (6-methoxyl and 8-hydroxyl) strongly suggested a 1,3-diaxial interaction effect of the fragmentation. The characteristic fragment ions were formed by the loss of water or acetic acid at position 8, irrespective of the stereochemistry at position 6. The possibility of distinct fragmentation mechanisms depending on the stereochemistry of the precursor ion could be discerned by recording the spectra in a deuterated solvent system of 0.05 hr ammonium acetate in D2O-acetonitrile-tetrahydrofuran. Loss of D2O from the precursor ion gave the fragment ion. This result indicated that the proton of protonation,vas included in the leaving water molecule, The peak intensity ratio R = [M + H](+)/[M + H - H2O](+) manifested the stereochemical differentiation of alkaloids at position 6. Copyright (C) 2000 John Wiley & Sons, Ltd.