Three-dimensional inversion of regional long-period magnetotelluric (MT) data reveals the presence of two distinct sets of high-conductivity belts in the Precambrian basement of the eastern U.S. Midcontinent. One set, beneath Missouri, Illinois, Indiana, and western Ohio, is defined by northwest–southeast-oriented conductivity structures; the other set, beneath Kentucky, West Virginia, western Virginia, and eastern Ohio, includes structures that are generally oriented northeast–southwest. The northwest-trending belts occur mainly in Paleoproterozoic crust, and we suggest that their high conductivity values are due to graphite precipitated within trans-crustal shear zones from intrusion-related CO₂-rich fluids. Our MT inversion results indicate that some of these structures dip steeply through the crust and intersect the Moho, which supports an interpretation that the shear zones originated as “leaky” transcurrent faults or transforms during the late Paleoproterozoic or the early Mesoproterozoic. The northeast-trending belts are associated with Grenvillian orogenesis and also potentially with Iapetan rifting, although further work is needed to verify the latter possibility. We interpret the different geographic positions of these two sets of conductivity belts as reflecting differences in origin and/or crustal rheology, with the northwest-trending belts largely confined to older, stable, pre-Grenville cratonic Laurentia, and the northeast-trending belts largely having formed in younger, weaker marginal crust. Notably, these high-conductivity zones spatially correlate with Midcontinent fault-and-fold zones that affect Phanerozoic strata. Stratigraphic evidence indicates that Midcontinent fault-and-fold zones were particularly active during Phanerozoic orogenic events, and some remain seismically active today, so the associated high-conductivity belts likely represent long-lived weaknesses that transect the crust.