In the framework of the Dead Sea Integrated Research project (DESIRE), 59 seismological stations were deployed in the region of the Dead Sea Basin. Twenty of these stations recorded data of sufficiently high quality between May and September 2007 to be used for ambient seismic noise analysis. Empirical Green’s functions are extracted from cross-correlations of long term recordings. These functions are dominated by Rayleigh waves, whose group velocities can be measured in the frequency range from 0.1 to 0.5 Hz. Analysis of positive and negative correlation lags of the Green’s functions makes it possible to identify the direction of the source of the incoming energy. Signals with frequencies higher than 0.2 Hz originate from the Mediterranean Sea, while low frequencies arrive from the direction of the Red Sea. Travel times of the extracted Rayleigh waves were measured between station pairs for different frequencies, and tomographically inverted to provide independent velocity models. Four such 2D models were computed for a set of frequencies, all corresponding to different sampling depths, and thus together giving an indication of the velocity variations in 3D extending to a depth of 10 km. The results show low velocities in the Dead Sea Basin, consistent with previous studies suggesting up to 8 km of recent sedimentary infill in the Basin. The complex structure of the western margin of the Basin is also observed, with sedimentary infill present to depths not exceeding 5 km west of the southern part of the Dead Sea. The high velocities associated with the Lisan salt diapir are also observed down to a depth of ~5 km. The reliability of the results is confirmed by checkerboard recovery tests.