Copyright © 2015 John Wiley & Sons, Ltd. Pyrazines are well-known natural products that are present in bacterial odours and food flavouring agents and are used as insect pheromones. Recently, a number of hydroxymethylpyrazines have been identified as thynnine wasp pheromones and orchid semiochemicals that are essential for pollination in sexually deceptive plants. These compounds are present in low amounts in complex blends, making GC-MS (including high-resolution techniques) the method of choice for their structure elucidation. We report the EI mass spectra for 14 representative compounds and have found that based on characteristic fragmentations, it is possible to distinguish between different positional isomers of hydroxymethylpyrazines. The presence or absence of either [M - 17]+, [M - 18]+· or [M - 19]+ fragment species provides characteristic information to allow the distinction between the different isomers. Considering the importance of pyrazines as a group of bioactive natural products, and the recent findings of biological activity for hydroxymethylpyrazines, our results presented here will aid the identification of these compounds in other biological systems.