Two coincident high-resolution airborne gravity and magnetic profiles of the Sudbury structure were forward modelled to better understand the geology of the structure at depth. A north–south profile was used to further investigate the deep geological setting of the Sudbury Igneous Complex (SIC) along Lithoprobe seismic transect, while an east–west profile was selected to examine a discontinuity in the magnetic and gravity fields near the centre of the SIC in the North Range. Constraints imposed on the best-fit model were the location of surface magnetic contacts, interpreted seismic and geological sections, and petrophysical data acquired from surface and borehole data. The constrained model computed for the north–south profile, elements of which are consistent with known Lithoprobe seismic reflectors, defines a north-verging fold in the deeper portion of the SIC. It may have developed during the modification of the initial geometry of the SIC by either a post-SIC thick-skinned basement shortening event, or by a compressive event that puts the tholeiitic basalts of the Elliot Lake Group against the SIC during the Penokean orogeny. The interpreted deep-seated basal folding explains the changes in dip of the seismic reflectors of the Archean basement and the SIC at about 4–8 km depth that were not fully accounted for in previous models of the Sudbury structure. This deformational event is interpreted to displace the base of the SIC rocks northwards to the depth of about 5 km, which is now reflected by a linear gravity high within the southern part of the Sudbury Basin. Lithological fence diagrams of the two interpreted sections, across and along a magnetic anomaly located in the northwest portion of the SIC, show that features of the observed anomaly pattern can be explained by a series of closely spaced deep-seated growth faults trending north around the Sandcherry fault, which has been previously interpreted as a reactivated pre-impact fault that affects the thickness and topography of both the SIC and highly magnetic Levack Gneiss Complex in that locality.