Infrared field-based reflectance spectroscopy in the Visible-Near-Infrared-Shortwave Infrared (VIS-NIR-SWIR) domain is a useful tool in mining geology particularly efficient for investigating the clay mineralogy of alteration haloes around ore deposits. It is used as a routine technique for the basic identification, mapping and semi-quantification of clay mineral species. However, the use of this technique for prospecting in hypogene deposits at depth in intertropical areas is strongly limited because of the presence of a thick, kaolinite-rich lateritic cover. Due to the strong IR absorption of kaolinite and the overlapping of its IR bands with those of most of the phyllosilicates in the SWIR domain, the use of field based near-infrared spectroscopy does not permit efficient identification and mapping of the phyllosilicates inherited from hypogene alteration that persist in the saprolite of lateritic profiles. In this paper, we propose a methodology to enhance the detection and semi-quantification of hypogene phyllosilicate minerals in kaolinite-rich lateritic saprolites using calibration curves. Those curves are built from the NIR spectra of binary admixtures of kaolinite or smectite with muscovite, Fe-Mg chlorite, clinochlore or talc in different known proportions. For each admixture series, calibration curves were established, based on investigation of two regions of interest within the NIR domain (1350–1470 nm and 2080–2500 nm) using a field-based spectrometer. For each binary mixture series of phyllosilicates, the second derivative of the NIR spectra was used to enhance the detection of the diagnostic absorption bands of each type of phyllosilicate, and hence to optimize the calculation of the intensity ratios between the diagnostic bands of the phyllosilicate components as a function of their percentage in the mixture. In presence of large amounts of lateritic kaolinite, the detection limit of the major types of hypogene phyllosilicates has been found at ranges from 5 to 10 wt% of the total clay content using the second derivative of the NIR spectra acquired with a field-based spectrometer. Above these aforementioned limits of detection, the semi-quantitative data obtained by comparing the NIR reflectance spectra of natural samples with those of the calibration curves could permit to map hypogene alteration haloes directly from the lateritic sa-prolite. Finally the described approach has been successfully tested on natural samples from the skarn deposits of the Ity gold mine (Ivory Coast).