ℇ⁶⁵Cu ([⁶⁵Cu/⁶³Cusample/⁶⁵Cu/⁶³CuNIST₋₉₇₆ -1]*10,000) in chalcopyrite from the 3 three igneous intrusions that make up the Grasberg Igneous Complex (GIC) and associated skarn deposits range from 0.2 to 13.4. Chalcopyrite grains from each intrusion have a specific range of ℇ⁶⁵Cu that is isotopically heavier in each successive intrusion. These variations may be interpreted in two ways: (1) isotope fractionation during distillation of Cu from the underlying source and establishment of hydrothermal cells associated with each intrusion; (2) isotope fractionation as the ore ore-bearing fluid moved outward from a central core. Within each sample, the smaller disseminated chalcopyrite grains yield consistently lower ℇ⁶⁵Cu values than larger disseminated grains, suggesting multiple mineralisation events. Chalcopyrite ℇ⁶⁵Cu from the Pyrite Shell, a sulfide-rich zone that surrounds the GIC, completely overlaps those from the three intrusions: suggesting that the source of Cu was the same. In contrast, while some chalcopyrite ℇ⁶⁵Cu values from the skarn deposits also overlap those from the GIC, a significant number are enriched in ⁶⁵Cu. These data may indicate that Cu within the skarns was derived from multiple sources or from multiple mineralisation events. ℇ⁵⁷Fe ([⁵⁷Fe/⁵⁴Fesample/⁵⁷Fe/⁵⁴FeIRMM₋₁₄ -1]*10,000) for pyrite and chalcopyrite range from -30.2 to 16.2. The ℇ⁵⁷Fe ranges of these two minerals do not overlap, suggesting that pyrite preferentially incorporated heavy Fe isotopes. ℇ⁵⁷Fe for GIC and skarn pyrite overlap, as do GIC and skarn chalcopyrite, suggesting genetic relationships. A large proportion of pyrite and chalcopyrite grains in the skarns also have low ℇ⁵⁷Fe values that do not overlap the igneous sulfides. This, coupled with the presence of pyrite grains with extremely low ℇ⁵⁷Fe values (ℇ⁵⁷Fe =-25), suggests that mixing between sedimentary and igneous Fe occurred during skarn replacement mineralisation. The chalcopyrite and pyrite Fe isotope data from the Pyrite Shell do not overlap those from the GIC, which indicates that Cu and Fe in the chalcopyrite were derived from different sources: the Cu is igneous, whereas the Fe is probably a mixture between sedimentary and igneous sources. The Cu and Fe isotope data from the Grasberg porphyry and skarn sulfides show that transition metal isotope variations occur within magmatic–hydrothermal systems, and that transition metal isotopes can become an important tool for interpretation of hydrothermal processes.