SUMMARY We present a new high-resolution 3-D shear wave velocity (Vs) model of the crust and uppermost mantle beneath Portugal, inferred from ambient seismic noise tomography. We use broad-band seismic data from a dense temporary deployment covering the entire Portuguese mainland between 2010 and 2012 in the scope of the WILAS project. Vertical component data are processed using phase correlation and phase weighted stack to obtain empirical Green functions (EGFs) for 2016 station pairs. Further, we use a random sampling and subset stacking strategy to measure robust Rayleigh-wave group velocities in the period range 7–30 s and associated uncertainties. The tomographic inversion is performed in two steps: First, we determine group-velocity lateral variations for each period. Next, we invert them at each grid point using a new trans-dimensional inversion scheme to obtain the 3-D shear wave velocity model. The final 3-D model extends from the upper crust (5 km) down to the uppermost mantle (60 km) and has a lateral resolution of ∼50 km. In the upper and middle crusts, the Vs anomaly pattern matches the tectonic units of the Variscan Massif and Alpine basins. The transition between the Lusitanian Basin and the Ossa Morena Zone is marked by a contrast between moderate- and high-velocity anomalies, in addition to two arched earthquake lineations. Some faults, namely, the Manteigas–Vilariça–Bragança fault and the Porto–Tomar–Ferreira do Alentejo fault, have a clear signature from the upper crust down to the uppermost mantle (60 km). Our 3-D shear wave velocity model offers new insights into the continuation of the main tectonic units at depth and contributes to better understanding the seismicity of Portugal.