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Iron formation-bearing sequences from the Guanhães Tectonic Block and Southern Espinhaço Belt of the Southeastern São Francisco Craton, were affected by the Ediacaran-Cambrian Brasilian Orogeny, when the Guanhães Block was upthrusted onto Statherian metasedimentary units of the Lower Espinhaço Supergroup. The iron formation contain a number of hydrothermal high-grade iron ore bodies (e.g. Horto-Baratinha, Cuité, Morro Escuro and Morro do Pilar deposits). Three different types of zircons were studied in order to characterize the temporal and geochemical evolution of the late-orogenic, hydrothermal event: detrital zircons (Lower Espinhaço Supergroup – Orosirian-Statherian maximum depositional age), zircons from the gneissic basement (Archean Guanhães Complex), and zircons from metagranitoid (Statherian Borrachudos Suite). All populations include zircons with <5 μm to 50 μm wide areas (mainly rims) that are brighter in BSE images. These zones are much younger than the rest of the grains (U-Pb SHRIMP ages from 492 Ma to 554 Ma) and display higher U contents and lower Th/U ratios. Zircons from pegmatites that crosscut the Paleoproterozoic sequence show similar ages, as well as high U contents and low Th/U ratios. Some of the pegmatite zircons contain inherited cores from the Borrachudos Suite. A general ZrO2, SiO2 and Th depletion and U, Pb, Hf, Mg, Ca, Fe, Yb and P enrichment was observed in the zircon rims in comparison with their cores. Lower εHf(t) values and higher 176Hf/177Hf(t) ratios were obtained in the zircon rims relative to the unaltered cores. Higher δ18O values (above 7‰) were found in the rims of the detrital and pegmatite zircons, being approximately 1‰ higher than the cores, indicating low-temperature water-rock interactions. Uplift and juxtaposition of Neoarchean gneissic rocks of the eastern São Francisco Craton, Statherian granites and metamorphic supracrustal units occurred during the late to mainly post-collisional stages of the Brasilian Orogeny (560–490 Ma). This uplift and decompression promoted partial melting of the Borrachudos Suite, generating pegmatite intrusions and a magmatic-hydrothermal fluid that affected the entire sequence. Zircons from metasedimentary rocks, granite and gneiss underwent recrystallization generally at sub-solidus conditions during interaction with the moderate- to low-temperature hydrothermal fluid. A concentric porous fabric is present in some grains and registers the fluid pathways during crystal alteration and recrystallization. This recrystallization process had a large impact on the chemical and isotopic compositions of the zircons. The pegmatite zircons represent new anatectic, zircon growth or anatectic overgrowth on older cores in the presence of fluid-saturated melts.