Abstract The damaging effects of electronic excitation, charging and beam heating during Auger electron spectroscopy (AES) are treated. The origin, manifestation and practical consequences of the phenomena are reviewed. A damage threshold, or critical dose, for beam damage due to electronic excitation is derived and related to experimental parameters. The close correlation between the predicted thresholds and the critical doses for damage observed in typical AES analyses indicates that primary excitation processes dominate the beam damage mechanism. Charging and the electromigration of ions in glasses are also discussed in detail. It is suggested that AES analyses of materials with potential susceptibility to beam damage be executed and interpreted with caution.