Sample heating during preparation of electron-thin specimens for observation in transmission electron microscopy (TEM) can produce artefacts which invalidate observations. This is particularly true of two-phase materials such as metal matrix composites, for which sample cooling with liquid nitrogen cannot be used to preserve the substructure during milling. A series of experiments is conducted using an age-hardenable aluminium alloy which produces a trace of peak temperature attained by TEM specimens during ion milling. It is shown that peak temperatures of the order of 650 K can be attained using conventional milling parameters; the technique must therefore be used with caution with materials such as metal matrix composites. A simplified one-dimensional heat transfer analysis of the problem is conducted to show that the most critical parameter is heat transfer along the sample holder legs and across interfaces along the heat path. Temperature differentials within the TEM specimen are shown to be less significant, yet these alone are capable of reaching 60 K within a dimpled specimen under usual milling conditions.