Several 5,6-dialkyl-2,4-diarylpyrimidines were prepared and their electron ionization (EI) mass spectra reported. The benzylic cleavage takes place easily together with an important McLafferty rearrangement. The involvement of the nitrogen atom appears to be important in the fragmentation of 5-methyl-substituted pyrimidines. In contrast, the 6-methyl-substituted pyrimidines undergo benzylic cleavage without hydrogen transfer. Thus, the difference in the mass spectrometric behaviour allows the identification of these isomeric compounds which, in contrast, exhibit only small differences in their NMR spectra. Copyright 1999 John Wiley & Sons, Ltd.