Au and As concentrations in pyrite grains from the Hishikari deposit were extensively determined by secondary ion mass spectrometry (SIMS) and electron probe microanalysis (EPMA) to investigate the microscale relationship between Au and As. The low-sulfidation epithermal Hishikari deposit, which has produced more than 224 t of gold since 1985 (as of March 2016), is world-famous for its high-grade ore. Accurate quantitative SIMS analyses of Au in pyrite were possible by preparing an Au-implanted pyrite standard sample and by using a properly tuned SIMS analytical method. An analysis size of 3 μm was chosen since the pyrite grains from the Hishikari deposit have heterogeneous As concentrations. This paper presents the first comprehensive data set of Au and As concentrations in a 3 μm area of pyrite obtained from the widely distributed high-grade Au-bearing Hishikari veins.Microanalyses of arsenian pyrite from the Hishikari gold deposit by SIMS and EPMA revealed that Au concentrations of 0.1–2800 ppm are positively correlated with As concentrations of 0 to 7 wt% in a 3 μm area. The formation of Hishikari veins is divided into two stages that are further subdivided into the early and late sub-stages. The rim of a pyrite grain precipitates after formation of the core; however, the time scale of core and rim formation is far shorter than that of the entire mineralization sequence. The specific value of the Au/As ratio in pyrite proves to be characteristic of the specific Au-bearing vein and its specific depth. Therefore, it could be possible to infer the nature of unknown veins by the Au/As ratio obtained. Although the Au/As ratio varies from vein to vein, a general tendency is observed for each ore zone of the Hishikari deposit. The Au/As ratio is high in the Sanjin ore zone, which consists of numerous high-grade veins in or above the Cretaceous accretionary sedimentary rocks of the Shimanto Group. The Au/As ratio is moderate in the Honko ore zone, which consists of several high-grade veins and also occurs in or above the basement sedimentary rocks. On the other hand, the Yamada ore zone, which consists of relatively low-grade veins, occurs in Pleistocene andesitic pyroclastic rocks that overlie the basement sedimentary rocks unconformably. The Au/As ratio in pyrite of the Yamada ore zone is relatively low compared with that of other ore zones.Several previous papers have proposed that the As− in pyrite may contribute to the reduction of Au+ to Au0 as Au nanoparticles (NPs) by As oxidation; however, Au and As concentrations of arsenian pyrites fall on or below the Au solubility limit in this study. Moreover, the As and S concentrations in pyrite are inversely correlated, which is consistent with the substitution of As for S as anionic As− in the Fe(S1−xAsx)2 solid solution of natural arsenian pyrite under reducing environments. The present study suggests that the Hishikari Au exists as a solid solution in the Hishikari arsenian pyrite, although there remains a possibility that it exists partially in the form of NPs even though the Au and As concentrations of arsenian pyrites fall on or below the Au solubility limit.