The association between trace elements and saprolite minerals has been investigated at the Boddington gold deposit and Scuddles massive Cu-Zn sulphide deposit in Western Australia by in situ laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and electron microprobe. The study provides new information about the occurrence and abundance of base metals, gold and their pathfinders in clay and ferruginous materials. Traces are predominantly located in vermiculite, interstratified clay minerals (chlorite–vermiculite and chlorite–smectite), goethite, hematite and titanium oxides. Although kaolinite is the main constitutent of saprolite, it retains insignificant amounts of trace elements and therefore dilutes geochemical anomalies. Anatase and rutile host abundant trace elements used as pathfinders for Au mineralization at Boddington (W, Bi and Mo) and base metal mineralization at Scuddles (Sb and Bi). As a result, the relative accumulation of these resistate minerals during weathering inflates pathfinder geochemical signatures. LA-ICP-MS compositional depth profiling obtained on conventional thin sections has proved to be an efficient tool to determine element–mineral associations in weathered material and to measure trace element concentrations. It allows a rapid detection of inclusions and highlights the distribution of trace elements between mineralogical phases.