We evaluate the use of the magnetotelluric (MT) method to locate crystalline basement and overlying carbonate reservoir rocks underneath a thick overburden in the São Francisco basin in Brazil. Mapping the complex basement and the carbonate reservoir using seismic reflection is a major problem in hydrocarbon exploration in this intracratonic basin, and it is expected that MT will provide useful complementary information. In the present study, we analysed 31 MT soundings along four survey lines in the central region of the basin. The MT soundings covered a period range of 0.001–100 s, probing the subsurface resistivity structure down to a maximum depth of about 15 km. The MT data were inverted using a regularized two-dimensional (2D) inversion algorithm with a variety of a priori data for comparison. For model appraisal, we analysed well log (gamma ray, deep resistivity and neutron porosity) data as well as seismic, gravity and magnetic profiles coincident with one MT line passing through the well. We found that shallow geological boundaries separating zones of strong resistivity contrasts also coincide with seismic boundaries in the inversion models with or without a priori data. Using gravity data, it was also possible to define the compartmentalized basement in this sector of São Francisco Basin, not clear in the seismic section. However, only by integrating all available information were we able to map the Lagoa do Jacaré and Sete Lagoas carbonate member-formations of the Bambuí Group, which are considered to host both the source and reservoir rocks identified from past exploratory history of this basin. We also imaged a basement structural high with thinned or disrupted conductive cover rocks over a known zone of hydrocarbon microseepage and a buried conductive (source rock?) channel at its NW margin, the trace of which coincides with the present-day River Paracatu along which gas bubbles have been observed. This suggests that MT may be fruitfully integrated with gravity, magnetic and seismic data to study the structural controls on hydrocarbon occurrence in this basin.