Diastereomeric conduramine derivatives, i.e., (1R,2S,3R/S,6S)-6-(N-carbomethoxyamino) 1,2-O-isopropylidenecyclohex-4-ene-1,2,3-triol (1 and 2) and their O-acetyl derivatives (3 and 4), were studied using gas chromatography (GC) with electron ionization (EI) and chemical ionization (CI). The EI mass spectra of diastereomeric pairs show consistent differences in the relative abundances of characteristic ions. The EI fragmentation patterns are based on precursor/product ion spectra, high-resolution mass spectrometry (HRMS) and deuterium labelling. The CI spectra show differences from the EI spectra, and the isobutane/CI spectra are much simpler than the methane/CI spectra. The differences shown in the CI spectra are similar to those shown in the product ion spectra of [M+H](+) ions generated under electrospray ionization (ESI) conditions. Theoretical calculations are performed to understand the observed differences. The differences in the relative stabilities of molecular ions, or protonated molecules at different sites, can explain the observed differences in the spectra.