“Invisible gold” in pyrite is defined as an Au solid solution of the pyrite lattice, sub-microscopic Au nanoparticles (NPs) in the pyrite, or other chemisorption complexes of Au. Because the relationship between the Au and As concentrations in pyrite could indicate the genesis of the deposit, the purpose of this study is to assess the micro-analytical characteristics of the Au–As relationship in pyrite from epithermal and hydrothermally affected sedimentary Au deposits by secondary ion mass spectrometry. The Au and As concentrations in pyrite vary from 0.04 to 30 ppm and from 1 to 1000 ppm, respectively, in the high-sulfidation Nansatsu-type epithermal deposits; these concentrations are both lower than those of the low-sulfidation epithermal Hishikari deposit. The Au concentrations in pyrrhotite and pyrite reach 6 and 0.3 ppm, respectively, in the Kalahari Goldridge banded-iron-formation-hosted gold deposit, and Au in pyrrhotite may sometimes exist as NPs, whereas As concentrations in pyrrhotite and pyrite are both low and lie in a narrow range from 6 to 22 ppm. Whether Au is present as NPs is important in ore dressing. The Au and As concentrations in pyrite from the Witwatersrand gold field range from 0.02 to 1.1 ppm and from 8 to 4000 ppm, respectively. The shape of the pyrite grains might prove to be an indicator of the hydrothermal influence on deposits of sedimentary origin, which implies the genesis of the deposits.