The subject of this paper concerns the seismic modelling of the crustal structure in the transition zone from the Bohemian Massif, across the Molasse basin and the Eastern Alps to the Southern Alps, mainly on the territory of Austria. The CEL10/Alp04 profile crosses the triple point of the European plate, Adriatic microplate and the recently identified Pannonian fragment. The seismic data along the presented profile originate from two large experiments: CELEBRATION 2000 and ALP 2002. The wavefield observed in the Eastern Alps is more complex than in the Bohemian Massif. Strong first arrivals (Pg) are distinct up to 60–90 km offset and are characterized by large variations in apparent velocity and amplitude. The contact between the Molasse basin and the Eastern Alps represents a barrier for seismic waves. Mid-crustal reflections (Pc) are usually recorded at short distance intervals (20–50 km) and are also characterized by variations in apparent velocity and amplitude. The Moho reflections are usually strong and well correlated, while Pn arrivals are only fragmentarily recorded. Detailed 2-D forward modelling of all refracted, post-critical and reflected phases, identified in the correlation process, was undertaken using a ray-tracing technique. The P-wave velocity in the crystalline upper crust of the Bohemian Massif and Molasse basin is about 6.15 km s−1, which is slightly higher than in the Alpine area (about 6.0 km s−1). Below the northern accretionary wedge of the Eastern Alps low-velocity sediments penetrate towards the southwest (SW) down to about 10 km depth. In the middle crust of the Alpine part, a reflective zone was modelled by a lamellae structure with alternating high and low velocities and thicknesses of about 2–3 km. The lower crust in this part of the model is more homogeneous, with a velocity of about 6.9 km s−1. In the Bohemian Massif, a high-velocity (HV) body (VP ∼ 7 km s−1) of a few kilometres thickness was delineated in the depth interval 18–23 km. The crustal thickness along the CEL10/Alp04 profile changes from about 42–44 km in the SW (Alpine part), to around 40 km in the central part of the profile (Molasse basin), and 38–40 km in the NE (Bohemian Massif). The velocity in the uppermost mantle determined from Pn wave traveltimes is about 8 km s−1 along the whole profile. The interpretation of the seismic wavefield is supplemented by an existing 3-D P-wave velocity model of the area. Main features derived by 2-D modelling (low velocities beneath the accretionary wedge, high velocities in the lower crust of the Bohemian Massif, Moho topography) well correlate with the 3-D model. Furthermore, the 3-D model allows assessing the lateral extent of significant features alongside the CEL10/Alp04 profile. This area is affected by both collision and escape tectonics. The high-reflectivity zone in the middle crust is explained by intermediate to mafic intrusions, rather than by ductile extensional deformation as generally observed in the lower crust.