We study the crustal structure under the Eastern and Southern Alps using ambient noise tomography. We use cross-correlations of ambient seismic noise between pairs of 71 permanent stations and 19 stations of the Eastern Alpine Seismic Investigation (EAST) profile to derive new 3D shear velocity models for the crust. Continuous records from 2014 and 2015 are cross-correlated to estimate Green's functions of Rayleigh and Love waves propagating between the station pairs. Group velocities extracted from the cross-correlations are inverted to obtain isotropic 3D Rayleigh- and Lovewave shear-wave velocity models. Our models image several velocity anomalies and contrasts and reveal details of the crustal structure. Velocity variations at short periods correlate very closely with the lithologies of tectonic units at the surface and projected to depth. Low-velocity zones, associated with the Po and Molas se sedimentary basins, are imaged well to the south and north of the Alps, respectively. We find large high-velocity zones associated with the crystalline basement that forms the core of the Tauern Window. Small-scale velocity anomalies are also aligned with geological units of the Austroalpine nappes. Clear velocity contrasts in the Tauern Window along vertical cross sections of the velocity model show the depth extent of the tectonic units and their bounding faults. A mid-crustal velocity contrast is interpreted as a manifestation of intracrustal decoupling in the Eastern Alps that accommodated eastward escape of the Alcapa block.