The late Cenozoic Baikal Rift Zone (BRZ) in southern Siberia is composed of several individual topographic depressions and half grabens with the deep Lake Baikal at its center. We have modeled the seismic velocity structure of the crust and uppermost mantle along a 360 km long profile of the Baikal Explosion Seismic Transects (BEST) project across the rift zone in the southern part of Lake Baikal. The seismic velocity structure along the profile is determined by tomographic inversion of first arrival times and 2-D ray tracing of first arrivals and reflections. The velocity model shows a gently deepening Moho from the Siberian Platform (41 km depth) into the Sayan-Baikal Fold Belt (46 km depth). We can exclude the presence of any Moho uplift around the ~10 km deep sedimentary graben structure of southern Lake Baikal. The lower crust includes a distinct 50-80 km wide high-velocity anomaly (7.4-7.6 ± 0.2 km/s), slightly offset to the northeast from the rift axis. We interpret this feature as resulting from mafic intrusions. Their presence may explain the flat Moho by compensation of lower crustal thinning by intrusion of mafic melts. The Pn wave velocities (8.15-8.2 km/s) are normal for the area and do not show any sign of decompression melting in the sub-Moho mantle, such that possible lithosphere thinning has not reached the base of the crust. On the basis of the results of the BEST project, we suggest that the BRZ is formed by passive rifting in the rheologically weak suture between the Siberian Platform and the Amurian plate.