The Proterozoic Midcontinent Rift System (MCRS) is considered one of the most important tectonic features in North America and was formed during a continental breakup event at 1.1 Ga (billion years). The MCRS is totally covered by Phanerozoic sedimentary rocks except in the Lake Superior region. Consequently, the geological characteristics of the MCRS are primarily inferred from extrapolations from the outcrop areas, drill holes, and from a variety of geophysical investigations. Iowa has a large segment of the MCRS which to date has only been partially investigated geophysically with little information regarding the lower crustal and upper mantle structure under the rift. Gravity and magnetic data were analyzed where Bouguer gravity, total-intensity magnetic and residual gravity anomaly maps clearly outline the main rift system with maxima anomalies over the basalt and minima anomalies over the flanking rift basins. Four gravity and magnetic models, perpendicular to the MCRS were constructed. These two-dimensional models are constrained by previous gravity and magnetic models performed elsewhere on the MCRS, seismic reflection data, basement penetrating drillholes and broadband seismic models. Even though the models are nonunique, they support the presence of lower crustal underplating materials formed by the extrusion of large amounts of mafic material from the upper mantle. These underplating materials are related to the plume derived magma. These deep roots mafic intrusions help resolving the controversy about the nature of the well-defined anomalies present in the area.