We use ambient noise tomography to investigate the crust and uppermost mantle structure beneath the Carpathian-Pannonian region of Central Europe. Over 7500 Rayleigh wave empirical Green's functions are derived from interstation cross-correlations of vertical component ambient seismic noise recordings (2005-2011) using a temporary network of 54 stations deployed during the South Carpathian Project (2009-2011), 56 temporary stations deployed in the Carpathian Basins Project (2005-2007) and 100 permanent and regional broad-band stations. Rayleigh wave group velocity dispersion curves (4-40 s) are determined using the multiple-filter analysis technique. Group velocity maps are computed on a grid of 0.2° × 0.2° from a non-linear 2-D tomographic inversion using the subspace method. We then inverted the group velocity maps for the 3-D shear wave velocity structure of the crust and uppermost mantle beneath the region. Our shear wave velocity model provides a uniquely complete and relatively high-resolution view of the crustal structure in the Carpathian-Pannonian region, which in general is validated by comparison with previous studies using other methods to probe the crustal structure. At shallow depths (<10 km) we find relatively high velocities below where basement is exposed (e.g. Bohemian Massif, Eastern Alps, most of Carpathians, Apuseni Mountains and Trans-Danubian Ranges) whereas sedimentary areas (e.g. Vienna, Pannonian, Transylvanian and Foçsani Basins) are associated with low velocities of well defined depth extent. The mid to lower crust (16-34 km) below the Mid-Hungarian Line is associated with a broad NE-SW trending relatively fast anomaly, flanked to the NW by an elongated low-velocity region beneath the Trans-Danubian Ranges. In the lowermost crust and uppermost mantle (between 30 and 40 km), relatively low velocities are observed beneath the Bohemian Massif and Eastern Alps but the most striking features are the broad low velocity regions beneath the Apuseni Mountains and most of the Carpathian chain, which likely is explained by relatively thick crust. Finally, most of the Pannonian and Vienna Basin regions at depths >30 km are relatively fast, presumably related to shallowing of the Moho consequent on the extensional history of the Pannonian region. © The Authors 2013. Published by Oxford University Press on behalf of The Royal Astronomical Society.