We discuss the implications of a lithospheric model of the Moroccan Atlas Mountains based on topography, heat flow, gravity and geoid anomalies, taking into account the regional geology. The NW African cratonic lithosphere, some 160-180 km thick, thins to c. 80 km beneath the Atlas fold-thrust belts, in contrast with the shortening regime prevailing there since the early Cenozoic. This fact explains several geological and geophysical features as high topography with modest tectonic shortening, the occurrence of alkaline magmatism contemporaneous to compression, the absence of large crustal roots to support elevation, the scarce development of foreland basins, and a marked geoid high. The modelled lithosphere thinning is related to a thermal upwelling constrained between the Iberia-Africa convergent plate boundary and the Saharan craton. © 2005 Blackwell Publishing Ltd.