The Variscan basement of the Axial Zone is exposed at four different structural levels in two mantled gneiss domes of the Central Pyrenees. The Aston-Hospitalet dome reflects the deepest levels and is cored by large orthogneiss massifs. The Bossòst dome further west possesses a central Variscan granitoid pluton and represents the upper crustal levels. The two gneiss domes are separated by later E-W-trending faults into northern half-domes and southern antiformal structures. Kinematic and metamorphic studies show that uplift of the orthogneiss core started under a N-S compressional setting and continued during dextral transpression. SE-NW-trending lineations in metasediments of the western Aston dome, the deepest level, represent fabrics developed at deeper levels early during the main deformation. They are partially obliterated by later intruding Variscan plutons. Younger ESE-WNW-trending lineations are characteristic for easterly directed flat-lying shear zones developed under amphibolite facies conditions at the roof zone of the orthogneiss and overlying weaker metasedimentary mantle rocks in the Hospitalet dome, which facilitated uplift of the orthogneiss core. In the deeper roots within the Aston orthogneiss such shear zones are not observed. Likewise, ascending Variscan plutons caused doming and the development of shallowly eastward dipping shear zones with a top-to-the-east kinematics in the southern Bossòst dome, while at deeper levels in the northern dome half coaxial deformation within the contact aureole prevails. Orogen-parallel extension, recorded in WNW–ESE structures, is restricted to the interface of rigid orthogneiss cores and weaker metasedimentary mantle rocks, or thermally weakened metasedimentary mantle above ascending Variscan plutons, and occurred under an overall transpressional setting.