Near-infrared (NIR) and short-wavelength infrared (SWIR) hyperspectral imagery can be used to detect certain alteration minerals. At epithermal deposits, the formation of alteration minerals is, in theory, related to the mineralisation of gold and silver. In order to provide foundations for developing sensor-based sorting applications at a mine that exploits such a deposit, it was investigated if NIR-SWIR hyperspectral imagery can be used to distinguish between ore and waste particles by characterising the alteration mineralogy. Maps were produced from the NIR-SWIR hyperspectral images of 827 drill core samples that show mineral occurrences, mineral absorption feature intensities and characteristics of the iron oxide mineralogy. Partial least squares discriminant analysis (PLS-DA) was applied to the information contained in these maps to investigate if this information can be used to discriminate between ore and waste. The results showed that NIR-SWIR hyperspectral imagery could be used to segment a population of waste samples by detecting occurrences of pyrophyllite, dickite and/or illite. This result can be explained by the fact that these minerals are commonly deposited further away from the ore-bearing epithermal veins, while the absence of SWIR-active minerals or detected occurrences of alunite are more closely associated with these structures. The ability to identify waste with NIR-SWIR spectral sensors means there is potential that sensor-based sorting can be used to remove this waste from mineral processing operations. Additional research is still required to assess the economic feasibility of such a sensor-based sorting application.