Transmission electron microscopy (TEM) is widely used for the characterization of the microstructure of Hg1-xCdxTe epilayers. Traditional TEM sample preparation methods, which usually involve argon ion milling, can easily cause damage to the material, and the size and density of the induced defects depend on the milling conditions. In this work, the structural damage caused by argon ion milling of Hg1-xCdxTe epilayers has been investigated. Multilayer samples with different Hg concentrations, as grown by molecular beam epitaxy, and p-n heterojunctions, as grown by liquid-phase epitaxy, have been examined. It is shown that, in addition to the milling conditions, the extent of the ion-induced damage depends sensitively on the Hg concentration of the Hg1-xCdxTe alloy as well as the epilayer growth conditions (i.e., Hg rich or Te rich). A possible mechanism that explains these results is briefly discussed. (c) 2006 American Vacuum Society.