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The mass spectra of stereoisomers of polymethoxy cycloalkanes depend on the geometry of the molecular ions. The magnitude of the stereochemical effect is influenced by the stability of the cyclic molecular ions. Due to energetically favourable ring-fragmentations the effect is cancelled by vicinal methoxy substituents and diminished by a methyl group next to a methoxy substituent. Stereochemically controlled fragmentations are the eliminations of a methoxy group in the form of a methanol or formaldehyde molecule from the molecular ions. By an investigation of di- and trimethoxy cyclohexanes, specifically labelled with deuterium, it is shown that both reactions are initiated by a transfer of an H-atom from a carbinol-C-atom to an O-atom of a methoxy group. Whether or not these energetically favourable reactions will occur depends on how close the H- and O-atoms involved can approach each other in the possible conformations of the molecular ion. The stereochemical control of the fragmentation of 1,3-dimethoxy cyclopentane, containing a more or less fixed five membered ring is small, that of dimethoxy cycloheptanes with a flexible seven membered ring is of comparable magnitude as the steric effect in the mass spectra of cyclohexane derivatives.