The Basque country magnetic anomaly follows a NW-SE trend over the Basque country (northern Spain) with intensities up to 250 nT measured at 3000 m above sea level. The paired negative part of the anomaly is located to the north and presents intensities down to −60 nT. A model of the magnetic properties of the crust in the area, taking into account previous geological and geophysical data, indicates a wedge of material with a magnetic susceptibility of 0.07 SI emplaced along a NE-directed basal thrust. The anomalous wedge is composed of basic and/or ultrabasic Cretaceous intrusives and lower crustal rocks, and reaches a minimum depth which increases towards the northwest from 5–7 to 12 km. According to previous works, geological features of the rocks on top of the anomalous wedge indicate that during the Cretaceous this zone constituted a deep marine environment which underwent important crustal thinning related to rifting. The transition towards the southwest was to a normal continental platform. Alpine deformation gave rise to displacement on a basal thrust, which can be correlated with the lower contact of the magnetic wedge, and emplacement of this wedge towards the northeast. The southeastern termination of the anomaly can be related to the lateral termination of the basic rocks which constitute the anomalous wedge in a transform fault related to the rifting event.