The Carboniferous Pajingo Epithermal System (PES) comprises several low sulphidation Au–Ag ore zones that have a total resource of c. 3 Moz (million ounces). The main Vera–Nancy vein is hosted by andesite that contains alteration which zones from inner silica–pyrite to argillic to distal propylitic alteration. Pyrite is ubiquitous in both alteration and vein. In the latter, pyrite is a minor component (<1%), but the dominant sulphide, and occurs as fine-grained (<50 μm) bands or disseminations. Coarse (up to 0.5 mm) euhedral pyrite is most abundant (up to 10%) in the silica–pyrite alteration whereas in argillic alteration pyrite (<50 to 250 μm) occurs as round to subhedral forms either as infill in narrow veinlets or as replacement. Fine-grained (<50 μm) pyrite occurs in propylitic alteration along rims of earlier mafic phenocrysts and has a low abundance (<1%). In-situ laser ablation inductively coupled plasma mass spectrometry was carried out on the pyrite in order to test the chemical variations between pyrite in different alteration zones. Results indicate that Mo and Ag concentrations vary over two orders of magnitude from the outer alteration zones (Mo c. 0.1 ppm; Ag c. 0.5 ppm) to the proximal vein alteration (Mo c. 30 ppm; Ag c. 20 ppm) whereas Pb displays an overall decrease from the hanging wall (a few hundred ppm) to the footwall (<100 ppm). Pyrite in the hanging- wall argillic alteration zone has Pb/Mo and Pb/Ag ratios of >100 whereas pyrite in silica–pyrite alteration zones has ratios of <100, and pyrite in silica–pyrite alteration zones immediately adjacent to the vein has Pb/Mo ratios of <30 and Pb/Ag ratios of <10. Thus, Pb/Mo and Pb/Ag ratios may provide a potentially powerful vector to epithermal gold veins in the PES and elsewhere.