In the present work we report results of a regional scale investigation of the thermal and magnetic characteristics of the crust in the southern sector of the geologic provinces of Tocantins and São Francisco, Brazil. Updated compilations of aeromagnetic and geothermal data sets were employed for this purpose. Use of such techniques as vertical derivative, analytic signal, and Euler deconvolution in analysis of aeromagnetic data has allowed precise locations of the sources of magnetic anomalies and determination of their respective depths. The anomalies in the Tocantins province are considered as arising from variations in the magnetic susceptibilities and remnant magnetizations of alkaline magmatic intrusions of the Tertiary period. The lateral dimensions of the bodies are less than 10 km, and these are found to occur at shallow depths of less than 20 km. On the other hand, the anomalies in the cratonic areas are related to contrasts in magnetic properties of bodies situated at depths greater than 20 km and have spatial dimensions of more than 50 km. Analysis of geothermal data reveals that the cratonic area is characterized by geothermal gradients and heat flow values lower when compared with those of the Tocantins province.