As part of a research programme to establish an analytical method for the simultaneous detection of the five major opium alkaloids in poppy seeds by liquid chromatography–electrospray ionization–mass spectrometry (LC-ESI-MS) it was discovered that the inclusion of thebaine produced two peaks for the same compound. This was in contrast to the effective simultaneous detection, by LC-ESI-MS, of morphine, codeine, papaverine and noscapine. The presence of these two peaks for thebaine was investigated using nuclear magnetic resonance spectroscopy with deuterated solvents to emulate the mobile phase conditions experienced. It was found that the presence of 80%, or higher ratios of, water caused two epimeric forms of thebaine to be formed; this explained the presence of two peaks on the chromatogram. In contrast, when a lower water content was used with 1% acetic acid, one stable form of thebaine could be analysed and resulted in a single peak visible in the subsequent chromatography.