Physical properties and compositions of ore-forming fluids in magmatic-hydrothermal systems have been mostly investigated by conventional fluid inclusion studies in transparent gangue minerals that are assumed to be “co-genetic” with the mineralization. However, ore precipitating fluids can be directly studied by analyzing fluid inclusions in opaque ore minerals, such as wolframite, stibnite, pyrite and enargite, by using near-infrared (NIR) petrography and microthermometry in combination with laser ablation-inductively coupled plasma mass spectrometry (LA-ICP-MS) analysis of individual inclusions. Although results of NIR fluid inclusion studies of ore minerals were first published in 1984, the technique is still not commonly used in fluid inclusion research due to a number of limitations related to the analytical equipment used, sample preparation and NIR mineral transmittance. In this contribution we present new data on the applicability of NIR fluid inclusion studies in ore minerals (pyrite, stibnite, enargite, and wolframite) from a series of magmatic-hydrothermal systems, according to their chemical composition and physical behavior during microthermometry. Our results reveal strong correlation between NIR transmittance and high trace element (Co, Ni, Cu, As) content in pyrite, enargite (Fe, Bi), and wolframite (Sc, V, Fe). Despite this, the restricted distribution of these elements in oscillatory and sector zoning has allowed observation of NIR mineral features and fluid inclusions. Energy absorption of opaque minerals, either as light energy during microscopy or as thermal conductive energy during fluid inclusion microthermometry, presents a second limitation for NIR fluid inclusion studies. Our results confirm the relevance of fluid inclusion studies in ore minerals by combining NIR microscopy and microthermometry. Despite some limitations due to trace element composition of the host mineral and its physical behavior at high temperature, a successful NIR fluid inclusion study can be performed on some ore minerals that are opaque in the visible light range, allowing the direct study of hydrothermal ore-forming fluids.